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A question appears when working with vcf file produced by UnifiedGenotyper on multiple samples. It is of course better to work with single sample vcf file so I was trying to split the multiple sampel vcf file. I used vcf-subset of vcftools but the problem is that the splitted single sample vcf file still has homozygous reference calls. Does anyone has a easy solution to this problem?
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Have you tried the -e parameter? I suppose -a should also be used to get rid of alternate alleles not found in the subset.
Here is the usage of vcf-subset:
Usage: vcf-subset [OPTIONS] in.vcf.gz > out.vcf
Options:
-a, --trim-alt-alleles Remove alternate alleles if not found in the subset
-c, --columns <string> File or comma-separated list of columns to keep in the vcf file. If file, one column per row
-e, --exclude-ref Exclude rows not containing variants.
-f, --force Proceed anyway even if VCF does not contain some of the samples.
-p, --private Print only rows where only the subset columns carry an alternate allele.
-r, --replace-with-ref Replace the excluded types with reference allele instead of dot.
-t, --type <list> Comma-separated list of variant types to include: SNPs,indels.
-u, --keep-uncalled Do not exclude rows without calls.
-h, -?, --help This help message. -
Thanks Gig77 for the answer! I tested with -e and it gave what I wanted.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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