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_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)
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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