cat C1_2L_all_SNPs_150818.vcf C1_2R_all_SNPs_150818.vcf C1_3L_all_SNPs_150818.vcf C1_3R_all_SNPs_150818.vcf C1_X_all_SNPs_150818.vcf C1_dmel_mitochondrion_genome_all_SNPs_150818.vcf > C1_all_SNPs_pre.vcf 

grep -v '#CHROM' C1_all_SNPs_pre.vcf > C1_all_SNPs.vcf 

rm C1_all_SNPs_pre.vcf

#############


awk '
    FNR==1 && NR!=1 { while (/^V1\tV2\tV3\tV4\tV5\tV6\tstart_obs\tstart_mle\tstart_lower\tstart_upper\tend_obs\tend_mle\tend_lower\tend_upper\tstart_limit\tend_limit\tsig_test\tlynch_chi_val\tlynch_p/) getline; }
    1 {print}
' MB_D5_lynch_for_fet_sig_snps_150820*.txt > D5_lynch_for_fet_sig_snps_150820.txt


#############

awk '
    FNR==1 && NR!=1 { while (/^V1\tV2\tV3\tV4\tV5\tV6\tmain\talt\tstartfreq\tendfreq/) getline; }
    1 {print}
' MB_D5_all_freq_change_150821*.txt > D5_all_freq_change_150821.txt


var="chr	pos	ref	MB_counts	C1_counts	C1_dec	C1_inc	C1_startfreq	C1_endfreq"
sed -i '' "1s/.*/$var/" C1_test.txt

# sed can't interpret tabs so instead paste the 'var' variable into the Terminal, 
#then go through and insert tabs using ctrl+v then tab.


############

awk '
    FNR==1 && NR!=1 { while (/^#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO/) getline; }
    1 {print}
' D3_*_fet_drift_sig_SNPs_150821.vcf > D3_fet_drift_sig_SNPs_150821.vcf


############

awk '
    FNR==1 && NR!=1 { while (/^#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO/) getline; }
    1 {print}
' CandS_*_all_SNPs_150908.vcf > CandS_all_SNPs_150908.vcf
