search

lh3 / psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
Other
156 stars 60 forks source link

Old pipeline deprecated, using bcftools consensus instead? #42

Open elizeng opened 2 years ago

elizeng commented 2 years ago

The pipeline to generate the input for psmc has always been samtools mpileup -C50 -uf ref.fa aln.bam | bcftools view -c - | vcfutils.pl vcf2fq -d 10 -D 100 | gzip > diploid.fq.gz

However, the pipeline is mostly deprecated by now and am wondering if anyone has started to use the updated consensus caller in bcftools consensus? The output is a .fa file instead of the .fq file, and wondered if that makes a difference.

Or if anyone can point me to a source for vcfutils.pl, I have tried bcftools 1.9 and 1.8, both of which do not seem to have this within...

francicco commented 2 years ago

Hi @elizeng

I'm having the same problem. Did you fix yours? Cheers F

elizeng commented 2 years ago

Hi @elizeng

I'm having the same problem. Did you fix yours? Cheers F

Hi @francicco I managed to find vcfutils.pl in bcftools 1.1. Hope that helps!

freshspaceoctopus commented 5 months ago

Hi, for anyone else looking for an alternative, I found that using samtools consensus can output a fastq file. You can turn on ambiguous bases so that heterozygous sites will be printed in your consensus.