Question: How to output all variant alleles at a given site, regardless of quality
0
gravatar for correlationmatrix
11 months ago by
correlationmatrix20 wrote:

How can one use either samtools mpileup or any other tool to, for a given position, output all alternate alleles regardless of quality? Just "samtools mpileup" (and the parameters I've tried so far) gives <*> for a position for which I observe an alternate base in IGV. (The purpose of doing this is for quality control)

mpileup snp variant • 337 views
ADD COMMENTlink modified 11 months ago by Brian Bushnell14k • written 11 months ago by correlationmatrix20
2
gravatar for Brian Bushnell
11 months ago by
Walnut Creek, USA
Brian Bushnell14k wrote:

You can do this with BBMap's CallVariants tool:

callvariants.sh in=mapped.bam ref=ref.fasta ploidy=2 vcf=all.vcf clearfilters

"clearfilters" sets all filters to zero, so no variant will fail. Your vcf file might be pretty big, though.

ADD COMMENTlink written 11 months ago by Brian Bushnell14k

Works! Although in this case I was only interested in looking up specific regions, but subsetting the BAM file using samtools first solves the problem. However, I got some Java errors when running callvariants.sh: "Invalid maximum heap size: -Xmx101593m. The specified size exceeds the maximum representable size.". Lowering the memory parameters to "-Xmx2048m -Xms2048m" still gave errors about "java.lang.OutOfMemoryError: Java heap space", but the program finished anyway and the output VCF seemed to look fine.

ADD REPLYlink written 11 months ago by correlationmatrix20

Oh... I'm guessing that you are using an older 32-bit version of Java? I suggest you upgrade to Java 8 64-bit version.

ADD REPLYlink written 11 months ago by Brian Bushnell14k

You're right, that was the issue!

ADD REPLYlink written 11 months ago by correlationmatrix20
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