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?
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