Hey,
I am looking for a way to add samples ID names to the FORMAT in my vcf file.
I have 10 sorted Bam files.
I used Freebayes to create vcf files and my next step is merging all 10 files for VcfSampleCompare. And for that I need to define groups that match the sample ID in the vcf file but here is one of my vcf file:
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each
allele">
##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation
count">
##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference
observations">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate
observations">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output
block.">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT **unknown**
NC_048323.1 461 . G T 28.0886 .AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=29;MQMR=0;NS=1;NUMALT=1;ODDS=6.46546;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=51;QR=0;RO=0;RPL=0;RPP=7.35324;RPPR=0;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:2:0,2:0:0:2:51:-4.01203,-0.60206,0
And I want to fix it to be like that:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/M1.sorted.bam /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/M3.sorted.bam /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/M5.sorted.bam /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/M7.sorted.bam /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/M9.sorted.bam /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/F1.sorted.bam /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/F2.sorted.bam /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/F4.sorted.bam /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/F6.sorted.bam /storage/users/IsanaRNA/FISH_DATA/MappingToAcipenserRuthenusGenome/results/Bam_sorted/F8.sorted.bam
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