Hi
I am seeing a seemingly incorrect somatic indel call using VarScan somatic.
The VarScan output line is
chr2 178883096 T +TAAC 11 0 0% T 6 2 25% */+TAAC Somatic 1 0.16374269 6 0 2 0 9 2 0 0
i.e. normal_reads2 = 0, yet the alignments and the pileup file show that the normal count is > 0. From the pileup file:
chr2 178883096 T 20 ...,...,....+4TAAC.+4TAAC.+3AAC.+3AAC.+4TAACC.+4TAAC.^KC ;;DHADDGEHH&1!!4!4.! 10 .......+4TAAC.+4TAACC. CDEEFF15!.
The parameters are:
samtools mpileup -f /home/enabieva/hg19/ucsc.hg19.fasta -A -E -q 1 $NORM $TUMOR >$OUT.pileup
java -jar ~/VarScan.v2.3.5.jar somatic $OUT.pileup $OUT.vs --mpileup 1 --tumor-purity 0.95
The VarScan version is 2.3.5
Anyone know what's going on?
Thanks.
I am seeing a seemingly incorrect somatic indel call using VarScan somatic.
The VarScan output line is
chr2 178883096 T +TAAC 11 0 0% T 6 2 25% */+TAAC Somatic 1 0.16374269 6 0 2 0 9 2 0 0
i.e. normal_reads2 = 0, yet the alignments and the pileup file show that the normal count is > 0. From the pileup file:
chr2 178883096 T 20 ...,...,....+4TAAC.+4TAAC.+3AAC.+3AAC.+4TAACC.+4TAAC.^KC ;;DHADDGEHH&1!!4!4.! 10 .......+4TAAC.+4TAACC. CDEEFF15!.
The parameters are:
samtools mpileup -f /home/enabieva/hg19/ucsc.hg19.fasta -A -E -q 1 $NORM $TUMOR >$OUT.pileup
java -jar ~/VarScan.v2.3.5.jar somatic $OUT.pileup $OUT.vs --mpileup 1 --tumor-purity 0.95
The VarScan version is 2.3.5
Anyone know what's going on?
Thanks.
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