Output from bcftools consensus in .fq format

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Feature
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
bioinformatics

Research direction

Start with the bcftools consensus command and compare its current FASTA output with the deprecated samtools mpileup, bcftools view, and vcfutils.pl vcf2fq pipeline described in the issue. Determine whether FASTQ output is supported or what command behavior and validation would be needed for a .fq.gz result.

Written by the indexing model from the issue text.

Description

enhancement

I am trying to run PSMC to obtain demographic history, and am looking to call consensus sequences from my study samples.

PSMC requires a ".fq.gz" input which is typically the whole-genome diploid consensus sequence of an individual.

The old pipeline, that is now deprecated that was recommended for generating the input file is:
samtools mpileup -C50 -uf ref.fa aln.bam | bcftools view -c - | vcfutils.pl vcf2fq -d 10 -D 100 | gzip > diploid.fq.gz

I have adapted my pipeline to use bcftools consensus instead but the pipeline seems to only output .fa files and not .fq files.

Is it possible to output a .fq file instead of only a .fa format.

Thanks!

Dominant language
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Merged PRs (30d)
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