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--sample-id does not work in force calling mode #427

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biorococo opened this issue Sep 6, 2023 · 0 comments
Open

--sample-id does not work in force calling mode #427

biorococo opened this issue Sep 6, 2023 · 0 comments

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@biorococo
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Output VCF from force calling ignores "--sample-id " parameter and just takes sample ID of the VCF used as input.

Command used:
$sniffles --input hg004.bam --sample-id HG004_regt --genotype-vcf input.vcf.gz --vcf output.vcf

Log:

_Running Sniffles2, build 2.2
Run Mode: genotype_vcf
Start on: 2023/09/06 13:28:59
Working dir: test
Used command: sniffles --input hg004.bam --sample-id HG004_regt --genotype-vcf input.cf.gz --vcf output.vcf

Opening for reading: hg004.bam
Opening for reading: input.cf.gz (read 751 SVs to be genotyped)
Opening for writing: output.vcf (single-sample, sorted)

Analyzing 329936 alignments total...

329936/329936 alignments processed (100%, 4391/s); 195/195 tasks done; parallel 0/4;
Took 75.14s.

Done._

Result:
$ cat output.vcf | grep CHROM
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG002

$ zcat input.vcf | grep CHROM
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG002

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