Old pipeline deprecated, using bcftools consensus instead?

[elizeng]

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]

Hi @elizeng

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

[elizeng]

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!