ERROR: Reference base(s) not correct. Is 'A', should be 'G'! - in line 86:
chr1	27360975	rs35659744	A	T	11836.9	undefined_filter	AB=0.51385;ABP=4.21333;AC=1;AF=0.5;AN=2;AO=371;CIGAR=1X;DP=722;DPB=722;DPRA=0;EPP=3.71852;EPPR=5.73856;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2590.13;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=13620;QR=12995;RO=351;RPL=71;RPP=309.949;RPPR=327.438;RPR=300;RUN=1;SAF=190;SAP=3.4844;SAR=181;SRF=185;SRP=5.24364;SRR=166;TYPE=snp;technology.ILLUMINA=1;CSQ=T|missense_variant|MODERATE|MAP3K6|MAP3K6|transcript|NM_004672.4|Coding|14/29|c.1866C>A|p.Asn622Lys|2135/4348|1866/3867|622/1288||,T|missense_variant|MODERATE|MAP3K6|MAP3K6|transcript|NM_001297609.1|Coding|13/28|c.1842C>A|p.Asn614Lys|2111/4324|1842/3843|614/1280||;dbNSFP_Polyphen2_HDIV_pred=B,B,.;dbNSFP_phyloP100way_vertebrate=0.029000,0.029000;dbNSFP_MutationTaster_pred=P,P;dbNSFP_Polyphen2_HVAR_pred=B,B,.;dbNSFP_SIFT_pred=T,.;ESP6500EA_AF=0.2959;ESP6500AA_AF=0.0572;1000G_AF=0.122005;EXAC_AF=0.223;COSMIC_ID=COSM1559292	GT:GL:DP:RO:QR:AO:QA	0/1:-1224.52,0,-1168.27:722:351:12995:371:13620
WARNING: FILTER 'undefined_filter' used but not defined! - in line 86:
chr1	27360975	rs35659744	A	T	11836.9	undefined_filter	AB=0.51385;ABP=4.21333;AC=1;AF=0.5;AN=2;AO=371;CIGAR=1X;DP=722;DPB=722;DPRA=0;EPP=3.71852;EPPR=5.73856;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=2590.13;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=13620;QR=12995;RO=351;RPL=71;RPP=309.949;RPPR=327.438;RPR=300;RUN=1;SAF=190;SAP=3.4844;SAR=181;SRF=185;SRP=5.24364;SRR=166;TYPE=snp;technology.ILLUMINA=1;CSQ=T|missense_variant|MODERATE|MAP3K6|MAP3K6|transcript|NM_004672.4|Coding|14/29|c.1866C>A|p.Asn622Lys|2135/4348|1866/3867|622/1288||,T|missense_variant|MODERATE|MAP3K6|MAP3K6|transcript|NM_001297609.1|Coding|13/28|c.1842C>A|p.Asn614Lys|2111/4324|1842/3843|614/1280||;dbNSFP_Polyphen2_HDIV_pred=B,B,.;dbNSFP_phyloP100way_vertebrate=0.029000,0.029000;dbNSFP_MutationTaster_pred=P,P;dbNSFP_Polyphen2_HVAR_pred=B,B,.;dbNSFP_SIFT_pred=T,.;ESP6500EA_AF=0.2959;ESP6500AA_AF=0.0572;1000G_AF=0.122005;EXAC_AF=0.223;COSMIC_ID=COSM1559292	GT:GL:DP:RO:QR:AO:QA	0/1:-1224.52,0,-1168.27:722:351:12995:371:13620
WARNING: INFO 'UNDEFINED_INFO' used but not defined! - in line 87:
chr1	45331833	rs3219489	C	G	3753.36	off-target	UNDEFINED_INFO=0.504386;ABP=3.0484;AC=1;AF=0.5;AN=2;AO=115;CIGAR=1X;DP=228;DPB=228;DPRA=0;EPP=26.1412;EPPR=26.5506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=847.076;OMIM=604933_[MUTYH_(provisional)_Adenomas,multiple_colorectal|Gastric_cancer,somatic|Colorectal_adenomatous_polyposis,autosomal_recessive,with_pilomatricomas];PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=4358;QR=4287,INVALID;RO=113;RPL=87;RPP=68.7398;RPPR=79.2809;RPR=28;RUN=1;SAF=53;SAP=4.53977;SAR=62;SRF=55;SRP=3.18325;SRR=58;TYPE=snp;technology.ILLUMINA=1;CSQ=G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001128425.1|Coding|12/16|c.1014G>C|p.Gln338His|1230/1930|1014/1650|338/549||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048174.1|Coding|12/16|c.930G>C|p.Gln310His|995/1695|930/1566|310/521||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293191.1|Coding|12/16|c.963G>C|p.Gln321His|1028/1728|963/1599|321/532||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293195.1|Coding|13/17|c.930G>C|p.Gln310His|1145/1845|930/1566|310/521||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048172.1|Coding|12/16|c.933G>C|p.Gln311His|1079/1779|933/1569|311/522||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048173.1|Coding|12/16|c.930G>C|p.Gln310His|1076/1776|930/1566|310/521||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293196.1|Coding|12/16|c.654G>C|p.Gln218His|1013/1713|654/1290|218/429||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048171.1|Coding|12/16|c.972G>C|p.Gln324His|1188/1888|972/1608|324/535||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293190.1|Coding|12/16|c.975G>C|p.Gln325His|1191/1891|975/1611|325/536||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293192.1|Coding|12/16|c.654G>C|p.Gln218His|1124/1824|654/1290|218/429||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_012222.2|Coding|12/16|c.1005G>C|p.Gln335His|1221/1921|1005/1641|335/546||;dbNSFP_Polyphen2_HDIV_pred=B,P,B,P,B,B,B;dbNSFP_phyloP100way_vertebrate=0.051000;dbNSFP_MutationTaster_pred=P;dbNSFP_Polyphen2_HVAR_pred=B,B,B,B,B,B,B;dbNSFP_SIFT_pred=T;HGMD_CLASS=DFP;HGMD_GENE=MUTYH;HGMD_ID=CM083726;HGMD_MUT=ALT;HGMD_PHEN="Reduced_activity";ESP6500EA_AF=0.2492;ESP6500AA_AF=0.2637;1000G_AF=0.313498;EXAC_AF=0.268;CLINVAR_ACC=RCV000034684.1|RCV000079500.3|RCV000131427.1|RCV000144634.1;CLINVAR_SIG=benign|benign|benign|benign;COSMIC_ID=COSM3751252	GT:GL:DP:RO:QR:AO:QA	0/1:-391.318,0,-384.928:228:113:4287:115:4358,INVALID
WARNING: For INFO 'QR' (number=1), the number of values is 2, but should be 1! - in line 87:
chr1	45331833	rs3219489	C	G	3753.36	off-target	UNDEFINED_INFO=0.504386;ABP=3.0484;AC=1;AF=0.5;AN=2;AO=115;CIGAR=1X;DP=228;DPB=228;DPRA=0;EPP=26.1412;EPPR=26.5506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=847.076;OMIM=604933_[MUTYH_(provisional)_Adenomas,multiple_colorectal|Gastric_cancer,somatic|Colorectal_adenomatous_polyposis,autosomal_recessive,with_pilomatricomas];PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=4358;QR=4287,INVALID;RO=113;RPL=87;RPP=68.7398;RPPR=79.2809;RPR=28;RUN=1;SAF=53;SAP=4.53977;SAR=62;SRF=55;SRP=3.18325;SRR=58;TYPE=snp;technology.ILLUMINA=1;CSQ=G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001128425.1|Coding|12/16|c.1014G>C|p.Gln338His|1230/1930|1014/1650|338/549||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048174.1|Coding|12/16|c.930G>C|p.Gln310His|995/1695|930/1566|310/521||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293191.1|Coding|12/16|c.963G>C|p.Gln321His|1028/1728|963/1599|321/532||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293195.1|Coding|13/17|c.930G>C|p.Gln310His|1145/1845|930/1566|310/521||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048172.1|Coding|12/16|c.933G>C|p.Gln311His|1079/1779|933/1569|311/522||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048173.1|Coding|12/16|c.930G>C|p.Gln310His|1076/1776|930/1566|310/521||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293196.1|Coding|12/16|c.654G>C|p.Gln218His|1013/1713|654/1290|218/429||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048171.1|Coding|12/16|c.972G>C|p.Gln324His|1188/1888|972/1608|324/535||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293190.1|Coding|12/16|c.975G>C|p.Gln325His|1191/1891|975/1611|325/536||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293192.1|Coding|12/16|c.654G>C|p.Gln218His|1124/1824|654/1290|218/429||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_012222.2|Coding|12/16|c.1005G>C|p.Gln335His|1221/1921|1005/1641|335/546||;dbNSFP_Polyphen2_HDIV_pred=B,P,B,P,B,B,B;dbNSFP_phyloP100way_vertebrate=0.051000;dbNSFP_MutationTaster_pred=P;dbNSFP_Polyphen2_HVAR_pred=B,B,B,B,B,B,B;dbNSFP_SIFT_pred=T;HGMD_CLASS=DFP;HGMD_GENE=MUTYH;HGMD_ID=CM083726;HGMD_MUT=ALT;HGMD_PHEN="Reduced_activity";ESP6500EA_AF=0.2492;ESP6500AA_AF=0.2637;1000G_AF=0.313498;EXAC_AF=0.268;CLINVAR_ACC=RCV000034684.1|RCV000079500.3|RCV000131427.1|RCV000144634.1;CLINVAR_SIG=benign|benign|benign|benign;COSMIC_ID=COSM3751252	GT:GL:DP:RO:QR:AO:QA	0/1:-391.318,0,-384.928:228:113:4287:115:4358,INVALID
WARNING: For INFO 'QR', the value 'INVALID' is not a 'Integer'! - in line 87:
chr1	45331833	rs3219489	C	G	3753.36	off-target	UNDEFINED_INFO=0.504386;ABP=3.0484;AC=1;AF=0.5;AN=2;AO=115;CIGAR=1X;DP=228;DPB=228;DPRA=0;EPP=26.1412;EPPR=26.5506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=847.076;OMIM=604933_[MUTYH_(provisional)_Adenomas,multiple_colorectal|Gastric_cancer,somatic|Colorectal_adenomatous_polyposis,autosomal_recessive,with_pilomatricomas];PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=4358;QR=4287,INVALID;RO=113;RPL=87;RPP=68.7398;RPPR=79.2809;RPR=28;RUN=1;SAF=53;SAP=4.53977;SAR=62;SRF=55;SRP=3.18325;SRR=58;TYPE=snp;technology.ILLUMINA=1;CSQ=G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001128425.1|Coding|12/16|c.1014G>C|p.Gln338His|1230/1930|1014/1650|338/549||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048174.1|Coding|12/16|c.930G>C|p.Gln310His|995/1695|930/1566|310/521||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293191.1|Coding|12/16|c.963G>C|p.Gln321His|1028/1728|963/1599|321/532||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293195.1|Coding|13/17|c.930G>C|p.Gln310His|1145/1845|930/1566|310/521||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048172.1|Coding|12/16|c.933G>C|p.Gln311His|1079/1779|933/1569|311/522||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048173.1|Coding|12/16|c.930G>C|p.Gln310His|1076/1776|930/1566|310/521||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293196.1|Coding|12/16|c.654G>C|p.Gln218His|1013/1713|654/1290|218/429||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048171.1|Coding|12/16|c.972G>C|p.Gln324His|1188/1888|972/1608|324/535||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293190.1|Coding|12/16|c.975G>C|p.Gln325His|1191/1891|975/1611|325/536||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293192.1|Coding|12/16|c.654G>C|p.Gln218His|1124/1824|654/1290|218/429||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_012222.2|Coding|12/16|c.1005G>C|p.Gln335His|1221/1921|1005/1641|335/546||;dbNSFP_Polyphen2_HDIV_pred=B,P,B,P,B,B,B;dbNSFP_phyloP100way_vertebrate=0.051000;dbNSFP_MutationTaster_pred=P;dbNSFP_Polyphen2_HVAR_pred=B,B,B,B,B,B,B;dbNSFP_SIFT_pred=T;HGMD_CLASS=DFP;HGMD_GENE=MUTYH;HGMD_ID=CM083726;HGMD_MUT=ALT;HGMD_PHEN="Reduced_activity";ESP6500EA_AF=0.2492;ESP6500AA_AF=0.2637;1000G_AF=0.313498;EXAC_AF=0.268;CLINVAR_ACC=RCV000034684.1|RCV000079500.3|RCV000131427.1|RCV000144634.1;CLINVAR_SIG=benign|benign|benign|benign;COSMIC_ID=COSM3751252	GT:GL:DP:RO:QR:AO:QA	0/1:-391.318,0,-384.928:228:113:4287:115:4358,INVALID
WARNING: For sample 'NA12878 / annotation 'QA' (number=A), the number of values is 2, but should be 1! - in line 87:
chr1	45331833	rs3219489	C	G	3753.36	off-target	UNDEFINED_INFO=0.504386;ABP=3.0484;AC=1;AF=0.5;AN=2;AO=115;CIGAR=1X;DP=228;DPB=228;DPRA=0;EPP=26.1412;EPPR=26.5506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=847.076;OMIM=604933_[MUTYH_(provisional)_Adenomas,multiple_colorectal|Gastric_cancer,somatic|Colorectal_adenomatous_polyposis,autosomal_recessive,with_pilomatricomas];PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=4358;QR=4287,INVALID;RO=113;RPL=87;RPP=68.7398;RPPR=79.2809;RPR=28;RUN=1;SAF=53;SAP=4.53977;SAR=62;SRF=55;SRP=3.18325;SRR=58;TYPE=snp;technology.ILLUMINA=1;CSQ=G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001128425.1|Coding|12/16|c.1014G>C|p.Gln338His|1230/1930|1014/1650|338/549||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048174.1|Coding|12/16|c.930G>C|p.Gln310His|995/1695|930/1566|310/521||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293191.1|Coding|12/16|c.963G>C|p.Gln321His|1028/1728|963/1599|321/532||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293195.1|Coding|13/17|c.930G>C|p.Gln310His|1145/1845|930/1566|310/521||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048172.1|Coding|12/16|c.933G>C|p.Gln311His|1079/1779|933/1569|311/522||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048173.1|Coding|12/16|c.930G>C|p.Gln310His|1076/1776|930/1566|310/521||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293196.1|Coding|12/16|c.654G>C|p.Gln218His|1013/1713|654/1290|218/429||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048171.1|Coding|12/16|c.972G>C|p.Gln324His|1188/1888|972/1608|324/535||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293190.1|Coding|12/16|c.975G>C|p.Gln325His|1191/1891|975/1611|325/536||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293192.1|Coding|12/16|c.654G>C|p.Gln218His|1124/1824|654/1290|218/429||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_012222.2|Coding|12/16|c.1005G>C|p.Gln335His|1221/1921|1005/1641|335/546||;dbNSFP_Polyphen2_HDIV_pred=B,P,B,P,B,B,B;dbNSFP_phyloP100way_vertebrate=0.051000;dbNSFP_MutationTaster_pred=P;dbNSFP_Polyphen2_HVAR_pred=B,B,B,B,B,B,B;dbNSFP_SIFT_pred=T;HGMD_CLASS=DFP;HGMD_GENE=MUTYH;HGMD_ID=CM083726;HGMD_MUT=ALT;HGMD_PHEN="Reduced_activity";ESP6500EA_AF=0.2492;ESP6500AA_AF=0.2637;1000G_AF=0.313498;EXAC_AF=0.268;CLINVAR_ACC=RCV000034684.1|RCV000079500.3|RCV000131427.1|RCV000144634.1;CLINVAR_SIG=benign|benign|benign|benign;COSMIC_ID=COSM3751252	GT:GL:DP:RO:QR:AO:QA	0/1:-391.318,0,-384.928:228:113:4287:115:4358,INVALID
WARNING: For sample 'NA12878 / annotation 'QA', the value 'INVALID' is not a 'Integer'! - in line 87:
chr1	45331833	rs3219489	C	G	3753.36	off-target	UNDEFINED_INFO=0.504386;ABP=3.0484;AC=1;AF=0.5;AN=2;AO=115;CIGAR=1X;DP=228;DPB=228;DPRA=0;EPP=26.1412;EPPR=26.5506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=847.076;OMIM=604933_[MUTYH_(provisional)_Adenomas,multiple_colorectal|Gastric_cancer,somatic|Colorectal_adenomatous_polyposis,autosomal_recessive,with_pilomatricomas];PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=4358;QR=4287,INVALID;RO=113;RPL=87;RPP=68.7398;RPPR=79.2809;RPR=28;RUN=1;SAF=53;SAP=4.53977;SAR=62;SRF=55;SRP=3.18325;SRR=58;TYPE=snp;technology.ILLUMINA=1;CSQ=G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001128425.1|Coding|12/16|c.1014G>C|p.Gln338His|1230/1930|1014/1650|338/549||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048174.1|Coding|12/16|c.930G>C|p.Gln310His|995/1695|930/1566|310/521||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293191.1|Coding|12/16|c.963G>C|p.Gln321His|1028/1728|963/1599|321/532||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293195.1|Coding|13/17|c.930G>C|p.Gln310His|1145/1845|930/1566|310/521||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048172.1|Coding|12/16|c.933G>C|p.Gln311His|1079/1779|933/1569|311/522||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048173.1|Coding|12/16|c.930G>C|p.Gln310His|1076/1776|930/1566|310/521||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293196.1|Coding|12/16|c.654G>C|p.Gln218His|1013/1713|654/1290|218/429||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001048171.1|Coding|12/16|c.972G>C|p.Gln324His|1188/1888|972/1608|324/535||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293190.1|Coding|12/16|c.975G>C|p.Gln325His|1191/1891|975/1611|325/536||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_001293192.1|Coding|12/16|c.654G>C|p.Gln218His|1124/1824|654/1290|218/429||,G|missense_variant|MODERATE|MUTYH|MUTYH|transcript|NM_012222.2|Coding|12/16|c.1005G>C|p.Gln335His|1221/1921|1005/1641|335/546||;dbNSFP_Polyphen2_HDIV_pred=B,P,B,P,B,B,B;dbNSFP_phyloP100way_vertebrate=0.051000;dbNSFP_MutationTaster_pred=P;dbNSFP_Polyphen2_HVAR_pred=B,B,B,B,B,B,B;dbNSFP_SIFT_pred=T;HGMD_CLASS=DFP;HGMD_GENE=MUTYH;HGMD_ID=CM083726;HGMD_MUT=ALT;HGMD_PHEN="Reduced_activity";ESP6500EA_AF=0.2492;ESP6500AA_AF=0.2637;1000G_AF=0.313498;EXAC_AF=0.268;CLINVAR_ACC=RCV000034684.1|RCV000079500.3|RCV000131427.1|RCV000144634.1;CLINVAR_SIG=benign|benign|benign|benign;COSMIC_ID=COSM3751252	GT:GL:DP:RO:QR:AO:QA	0/1:-391.318,0,-384.928:228:113:4287:115:4358,INVALID
WARNING: Unknown MISO term 'undefined_variant' used! - in line 88:
chr1	62247552	rs2941679	C	G	1166.14	off-target	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=37;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=4.47751;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=55.8981;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1438;QR=0;RO=0;RPL=37;RPP=83.3548;RPPR=0;RPR=0;RUN=1;SAF=16;SAP=4.47751;SAR=21;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;CSQ=G|undefined_variant|MODERATE|KANK4|KANK4|transcript|NM_181712.4|Coding|9/10|c.2803G>C|p.Val935Leu|3180/5477|2803/2988|935/995||;dbNSFP_Polyphen2_HDIV_pred=B,B;dbNSFP_phyloP100way_vertebrate=0.698000;dbNSFP_MutationTaster_pred=P;dbNSFP_Polyphen2_HVAR_pred=B,B;dbNSFP_SIFT_pred=T;ESP6500EA_AF=0.9598;ESP6500AA_AF=0.9923;1000G_AF=0.986222;EXAC_AF=0.974	GT:GL:DP:RO:QR:AO:UNDEFINED_FORMAT	1/1:-129.809,-11.1381,0:37:0:0:37:1438
WARNING: FORMAT 'UNDEFINED_FORMAT' used but not defined! - in line 88:
chr1	62247552	rs2941679	C	G	1166.14	off-target	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=37;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=4.47751;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=55.8981;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1438;QR=0;RO=0;RPL=37;RPP=83.3548;RPPR=0;RPR=0;RUN=1;SAF=16;SAP=4.47751;SAR=21;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;CSQ=G|undefined_variant|MODERATE|KANK4|KANK4|transcript|NM_181712.4|Coding|9/10|c.2803G>C|p.Val935Leu|3180/5477|2803/2988|935/995||;dbNSFP_Polyphen2_HDIV_pred=B,B;dbNSFP_phyloP100way_vertebrate=0.698000;dbNSFP_MutationTaster_pred=P;dbNSFP_Polyphen2_HVAR_pred=B,B;dbNSFP_SIFT_pred=T;ESP6500EA_AF=0.9598;ESP6500AA_AF=0.9923;1000G_AF=0.986222;EXAC_AF=0.974	GT:GL:DP:RO:QR:AO:UNDEFINED_FORMAT	1/1:-129.809,-11.1381,0:37:0:0:37:1438
ERROR: Reference base(s) not correct. Is 'C', should be 'T'! - in line 89:
chr1	94112992	99053	C	.	.	.	AB=0.99;ABP=3.4435	GT:GL:DP:RO:QR:AO:UNDEFINED_FORMAT	1/1:-129.809,-11.1381,0:37:0:0:37:1438
WARNING: Missing value '.' used as alternative allele! - in line 89:
chr1	94112992	99053	C	.	.	.	AB=0.99;ABP=3.4435	GT:GL:DP:RO:QR:AO:UNDEFINED_FORMAT	1/1:-129.809,-11.1381,0:37:0:0:37:1438
WARNING: First base of insertion/deletion not matching - ref: 'CTAGGGAAAAACATATACCCAT' alt: 'T'! - in line 90:
chr8	100717889	2193785	CTAGGGAAAAACATATACCCAT	T	.	.	AB=0.99;ABP=3.4435	GT:GL:DP:RO:QR:AO:UNDEFINED_FORMAT	1/1:-129.809,-11.1381,0:37:0:0:37:1438
