VCF output when merging with bcftools merge
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5.7 years ago
steven.davis ▴ 10

I am merging multiple single-sample VCF files into one multi-sample VCF file with bcftools merge using this command:

bcftools merge --info-rules NS:sum -o outFilePath dir/*.gz

Previously, using bcftools 1.1, the output VCF file contained one row per position, like this:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
barref  1094    .       A       G       .       PASS    NS=24
barref  1221    .       G       A       .       PASS    NS=24
barref  2015    .       G       A       .       PASS    NS=24

Using newer version of bcftools 1.2 or 1.3.1, I am seeing two rows per position, like this:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
barref  1094    .       A       .       .       PASS    NS=20
barref  1094    .       A       G       .       PASS    NS=4
barref  1221    .       G       .       .       PASS    NS=20
barref  1221    .       G       A       .       PASS    NS=4
barref  2015    .       G       .       .       PASS    NS=20
barref  2015    .       G       A       .       PASS    NS=4

First, should I be concerned about the change in output?

Secondly, I would prefer the old style with a single row per position. Does anyone know how to get one row of output per position when using bcftools 1.2 or higher?

vcf bcftools • 3.1k views
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5.7 years ago
steven.davis ▴ 10

Solved it with help from a colleague. Problem solved with "--merge all" command line option.

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Hey can you post the full command you used to solve this problem?

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