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lh3 / psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
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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 1 year ago

Hi @elizeng

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

elizeng commented 1 year 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 1 month 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.