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Warning from lumpyexpress when calling copy number variants

Hello,

I am running one of the most basic commands, found on the lumpy webpage:

lumpyexpress -B my.bam -S my.splitters.bam -D my.discordants.bam -o output.vcf

to call copy number variants.

One of the warnings that I received was "Warning: only 0 elements in distribution (min:1000). I dug around and found the actual code. Only problem is, I am a beginner in python and I am having trouble identifying what the elements are other than that they are in the L array. I was wondering if anyone have had experienced this problem before, what the "elements" are, and whether this will affect my results. I am still getting a growing vcf file as the output as we speak. Thanks!

cnv genome next-gen python lumpy
• 3,163 views • link
updated by Ram Ram • written by ehzed • ehzed

Maybe you have single-end data and it expects paired-end data?

• 1 views • link
written by trausch trausch

Hi trausch, I have paired end data

• 1 views • link
written by ehzed • ehzed

pairend_distro.py needs at least 1000 alignments to determine the stats that lumpy uses to id breakpoints. These alignments must:

  1. have the flags "read paired", "mast reverse strand", "first in pair" set

  2. not have the flags "read unmapped", "mate unmapped", "read reverse strand", "second in pair", "not primary alignment", "read is PCR or optical duplicate", "supplementary alignment"

  3. have an insert size >= 0

  4. have the chrom of both the alignment and mate match

In your case, none of the first 1000000 alignments met all of these criteria.

What did you use to align your data?

How did you align your bam?

• 1 views • link
written by Ryan Layer • Ryan Layer

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