bcftools: Wrong number of PL fields? nals=4 npl=6
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4.3 years ago

Hello all,

I am new to bcftools and samtools, so forgive my question if it is ignorant. My goal is to extract consensus sequences between two different species.

I was given paired-end Illumina sequencing data. So far, I used FastQC to trim and bowtie 2 to perform the mapping and used samtools to generate sorted bam files. We created two bam files by using single-ended bowtie 2 mapping - this was due to a large amounts of insertion-deletion polymorphisms between the two species.

I tried the following to variant call:

/home/sean/Desktop/assembly_software/samtools-1.3.1/samtools mpileup -d8000 -uf Mlongifolia_CMEN585_assembly_v1.0.fasta CMEN585.R_1.sorted.bam CMEN585.R_2.sorted.bam | bcftools call -c | vcfutils.pl vcf2fq > cnsnew.fq

error: Wrong number of PL fields? nals=4 npl=6

Then I tried using just a single bam file:

/home/sean/Desktop/assembly_software/samtools-1.3.1/samtools mpileup -d8000 -uf Mlongifolia_CMEN585_assembly_v1.0.fasta CMEN585.R_1.sorted.bam | bcftools call -c | vcfutils.pl vcf2fq > cnsnew.fq

error: Wrong number of PL fields? nals=4 npl=3

What do these error mean and how do I fix them? I have searched around, but have been unable to turn up anything so far.

I assume you need to variant call before you extract consensus sequences. I tried to extract the consensus sequences anyway (just for kicks):

/home/sean/Desktop/assembly_software/samtools-1.3.1/samtools \ mpileup \ -B \ -u \ -f Mlongifolia_CMEN585_assembly_v1.0.fasta\ CMEN585.R_1.sorted.bam | \ bcftools call -cg | \ vcfutils.pl vcf2fq \ ->R_1_consensus.fq

error: Use of uninitialized value $l in numeric lt (<) at /usr/local/bin/vcfutils.pl line 566. Use of uninitialized value $l in numeric lt (<) at /usr/local/bin/vcfutils.pl line 566.

Thank you for your help,

Richard

alignment sequencing bcftools samtools • 1.8k views
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