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)
Question: How to output all variant alleles at a given site, regardless of quality
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correlationmatrix • 20 wrote:
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modified 16 months ago
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Brian Bushnell ♦ 15k
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16 months ago by
correlationmatrix • 20
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Brian Bushnell ♦ 15k 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.
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.
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