bcftools isec not producing sites.txt
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7 days ago
steve ★ 2.9k

I am running a bcftools command like this;

bcftools isec -p /data --targets-file targets.bed Sample1.vcf.gz Sample2.vcf.gz

And I am getting output files like this;


There is no sites.txt file output.

Normally when I run other sets of samples in bcftools isec, I also get a file sites.txt which has just the genomic regions used for intersection, and which sample sample each variant was present in, like this;

$ head input/sites.txt
1       45799087        G       A       111
1       115256527       C       T       110
1       115256527       CTTG    TTTT    001
1       115256530       G       T       110
1       193099343       G       T       010
2       26101038        C       A       100

Since I am not getting this file output, its making it difficult to parse with my existing workflow. Instead, the README.txt file has a description this like;

This file was produced by vcfisec.
The command line was:   bcftools isec -p /data --targets-file targets.bed Sample1.vcf.gz Sample2.vcf.gz

Using the following file names:
/data/0000.vcf     for records private to  Sample1.vcf.gz
/data/0001.vcf     for records private to  Sample2.vcf.gz
/data/0002.vcf     for records from Sample1.vcf.gz shared by both       Sample1.vcf.gz Sample2.vcf.gz
/data/0003.vcf     for records from Sample2.vcf.gz shared by both    Sample1.vcf.gz Sample2.vcf.gz

Any idea why I am not getting the sites.txt file? Ultimately, I need to get the list of all variants from all input files, and the presence/absence of each variant in each file, like what sites.txt shows.

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