PSMC vcfutlis.pl vcf2fq is not supported?

[Priambodobagus]

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!

[pd3]

Just noting here that this was also requested in https://github.com/samtools/bcftools/issues/1670, and also see the comment https://github.com/samtools/bcftools/issues/1670#issuecomment-1061865432

[Sonalhooda]

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!

How did you proceed with your PSMC analysis ?