Varscan output contains dots

Question

[pulyakhina]

Hi guys,

I'm using VarScan v 2.3.7 to call SNPs in Illumina Hiseq2000 RNA-Seq paired-end sample:

> samtools mpileup -B -Q 0 -f reference.fa $CONTROL.bam > sample.mpileup
> java -jar VarScan mpileup2cns sample.mpileup --min-coverage 10 --min-reads2 3 --strand-filter 0 --output-vcf 1 > sample.vcf

What I get a lot is columns that contain dots at a position of the variance:

chr1 155979352 . A . . PASS ADP=464;WT=1;HET=0;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/0:666:536:464:448:14:3.03%:5.523E-5:37:34:315:133:14:0

When I check the reads in UCSC, I can see 448 A (reference allele), 14 G (alternative allele) and no other nucleotides. I'm not sure why, instead of reporting "G", Varscan reports a dot as a variance.

Does anyone have an explanation for this?

Thanks in advance!

Cheers,
Irina

[nnutter]

This question was cross-posted on SEQanswers.

[Ram]

Quick question: Why does the second command use $sample.mpileup? Should it not be simply sample.mpileup?

[pulyakhina]

Sorry, was copying it from a bash script and didn't remove all $ signs. But you are right, it's just sample.mpileup both in the first and in the second command.

[Ram]

OK, I made the change.

[Ram]

Hello pulyakhina!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?p=157132

This is typically not recommended as it runs the risk of annoying people in both communities. Thank you, nnutter, for the pointer.