How to output all variant alleles at a given site, regardless of quality

Question

[correlationmatrix]

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)

Answer 1

[Brian Bushnell]

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.

[correlationmatrix]

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.

[Brian Bushnell]

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.

[correlationmatrix]

You're right, that was the issue!