PSMC vcfutlis.pl vcf2fq is not supported?

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
25/100
Issue type
Feature
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

Start by reviewing the PSMC command in the issue and the current support for vcfutils.pl vcf2fq, bcftools call, and bcftools consensus. Compare the expected FASTQ output with the FASTA produced by the suggested consensus workflow; done means documenting or defining a supported conversion path for this pipeline.

Written by the indexing model from the issue text.

Description

enhancement

Hi I am running PSMC analysis, in their website (psmc github) is provided this command:
samtools mpileup -C50 -uf ref.fa aln.bam | bcftools view -c -
| vcfutils.pl vcf2fq -d 10 -D 100 | gzip > diploid.fq.gz

samtools mpileup already change into bcftools mpileup.
bcftools view already change to bcftools call.
but for vcfutils.pl vcf2fq is not supported anymore. anyone knows how I can convert the vcf to fastq format? some sites suggested to use bcftools consensus to substitute the vcf2fq (bcftools consensus). but this command was generating fasta format.
Please let me know if someone also working with PSMC these days!
Github, do your magic!

Dominant language
C
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Forks
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Avg merge
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Merged PRs (30d)
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