Question: Error in SAMTools mpileup
0
gravatar for julia92796
7 months ago by
julia927960
julia927960 wrote:

I have a BAM file containing an alignment of the neanderthal y chromosome to the human y chromosome. I'm trying to extract the consensus sequence of the neanderthal reads so that I can isolate genes. I found this command online:

samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq

and am trying to use it to output the consensus sequence. However, I keep getting an error:

Error: Could not parse --min-ac g Use of uninitialized value $l in numeric lt (<) at vcfutils.pl line 566.
Use of uninitialized value $l in numeric lt (<) at vcfutils.pl line 566.
<mpileup> Set max per-file depth to 8000

Does anyone know how to fix this? If not, is there an alternate method to get a consensus sequence from reads?

ADD COMMENTlink written 7 months ago by julia927960

I also encounter the similar problem, and haven't resolved this yet.

Is there anyone who knows what's wrong with this error?

Thanks a lot. : )

ADD REPLYlink written 6 months ago by galanhsnu0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1751 users visited in the last hour