Hi,
Tried to use VarScan 2 to get SNP calls (tumor/normal paired samples). However, I don't think the output makes sense.
For example, the pileup file for the normal looks like,
chr1 11765 N 6 GgGGGG AG@?AF
chr1 11766 N 6 TtTTTT AG6:4E
chr1 11767 N 6 GgGGGG CEBA=F
chr1 11768 N 6 TtTTTT CF@;AG
The VarScan 2 output:
chrom position ref var normal_reads1 normal_reads2 normal_var_freq normal_gt tumor_reads1
tumor_reads2 tumor_var_freq tumor_gt somatic_status variant_p_value somatic_p_value tumor_reads1_plus
tumor_reads1_minus tumor_reads2_plus tumor_reads2_minus
...
chr1 11766 N T 0 9 100% T 0 9 100% T Germline 1.101911
9461502356E-10 1.0 0 0 6 3 0 0 7 2
Not sure what went wrong when the pileup file show read count is 6 (bold) at location 11766, but the VarScan has a count of 9 (bold).
Thanks!
Tried to use VarScan 2 to get SNP calls (tumor/normal paired samples). However, I don't think the output makes sense.
For example, the pileup file for the normal looks like,
chr1 11765 N 6 GgGGGG AG@?AF
chr1 11766 N 6 TtTTTT AG6:4E
chr1 11767 N 6 GgGGGG CEBA=F
chr1 11768 N 6 TtTTTT CF@;AG
The VarScan 2 output:
chrom position ref var normal_reads1 normal_reads2 normal_var_freq normal_gt tumor_reads1
tumor_reads2 tumor_var_freq tumor_gt somatic_status variant_p_value somatic_p_value tumor_reads1_plus
tumor_reads1_minus tumor_reads2_plus tumor_reads2_minus
...
chr1 11766 N T 0 9 100% T 0 9 100% T Germline 1.101911
9461502356E-10 1.0 0 0 6 3 0 0 7 2
Not sure what went wrong when the pileup file show read count is 6 (bold) at location 11766, but the VarScan has a count of 9 (bold).
Thanks!
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