Combining multiple Streak variant files with their filename
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5 months ago

I am trying to concatenate multiple Strelka vcf files from different samples to one file. Using vcf-concat I was able to combine them. But, I also want to include their sample name/filename in the merged file, preferably as the first column. Is there a way to do that using VCFtools?

Code I used:

vcf-concat File1.vcf.gz File2.vcf.gz File3.vcf.gz | gzip -c > Merged.vcf.gz

Many thanks!

Parvathi.

NGS VCF Strelka2 • 283 views
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vcftools is deprecated use bcftools merge or bcftools concat

preferably as the first column.

uh ?

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Thank you for the reply.

Looks like, bcftools concat is similar to vcf-concat.

Regarding, "including the filename after concatenate?" When viewing the concatenated file I would like to know from which vcf file each row belongs to. So, thought about adding a new column with sample name. Not sure if it is possible. I am using Strelka vcf, the header won't have a sample name.

VCF, which looks like this:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR

chr12 92538217 . T G . PASS SOMATIC;QSS=496;TQSS=1;NT=ref;QSS_NT=3070;TQSS_NT=1;SGT=TT->GT;DP=1897;MQ=60.00;MQ0=0;ReadPosRankSum=0.37;SNVSB=0.00;SomaticEVS=19.87;CSQ=G|missense_variant|MODERATE|BTG1|ENSG00000133639|Transcript|ENST00000256015.3 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 610:5:0:0:0,0:0,0:0,0:605,611 1284:2:0:0:0,0:2,2:233,234:1047,1050

bcftools merge, will merge the variants in a column-wise manner, which I don't prefer.

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