Hello,
I have been struggling for several days now to get bcftools call to work for
me. I have 75 RAD-sequenced samples and I'm trying to test out some population
genomics analyses with samtools, bcftools, and vcftools. I've aligned my
filtered samples to a reference genome (with 3503 scaffolds) using bowtie2. For
each file I ran
samtools view -bS ${file}.sam | samtools sort - ${file}_sorted
and then
samtools mpileup -u -f allpaths_cms1.scaff_fixed.fa -b test_samples.txt |
bcftools call -mv -Ov > test.vcf
(where test_samples.txt is a list of all of the sorted files).
Every time after running the mpileup and bcftools call I get the error "Wrong
number of PL fields? nals = 4 npl = 225". There is a vcf file afterwards and it
contains data up until the midway point of one of the lines, where it cuts off
after 8 of the samples. Here is the line:
scaffold_53 654320 . T A 25.9053 .
DP=94;VDB=0.000411984;SGB=0.308018;MQ0F=0.978723;AC=10;AN=10;DP4=0,0,6,0;MQ=14
GT:PL ./.:0,0,0 ./.:0,0,0 ./.:0,0,0 ./.:0,0,0 1/1:13,3,0
./.:0,0,0 ./.:0,0,0 ./.:0,0,0
My understanding of this error is that for some reason, one of the individuals
apparently has 225 phred-scored likelihoods for only 4 alleles (although this
isn't even true for the last line in the file). But I can't figure out how to
fix it, if it's a bug or compatibility issue, or if I'm doing something wrong.
Is there a way to change which types of likelihoods are output to see if a
different type would eliminate the error?
I'm running samtools 1.2, bcftools 1.2, and htslib 1.2.1.
Can you help me identify the problem and fix it so that I can move forward with
my analysis?
Any help would be greatly appreciated!
Best regards,
Sarah
Sarah Flanagan
PhD Candidate
NSF Graduate Research Fellow and Texas A&M Merit Scholar
Jones Lab, Biology Department
Texas A&M University
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