VarScan.v2.3.2 output file format problem

[SD2010Bioinfo]

I'm using Varscan.v2.3.2 to do somatic variants calling in tumor-normal sample with command below. But the output snp and indel files have different columns between head line(19 columns) and content (23 columns). What do the extra 4 columns mean?

(command：java -Xmx3g -jar VarScan.v2.3.2.jar somatic chr17_N.mpileup chr17_T.mpileup --min-coverage 10 --min-coverage-normal 10 --min-coverage-tumor 10 --min-var-freq 0.2 --min-freq-for-hom 0.75 --somatic-p-value 0.05 --output-snp chr17.snp --output-indel chr17.indel)

chr17.snp
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
chr17 6115 G C 0 24 100% C 0 46 100% C Germline 1.0658598000218083E-41 1.0 0 0 4 42 0 0 11 13

--------------------------------------------------------------------------
chr17.indel
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
chr17 565264 A -T 9 7 43.75% */-T 9 14 60.87% */-T Germline 1.1401894182998399E-8 0.23331930373087006 0 9
0 14 0 9 0 7


Thank you!

[fbsja]

extra columns? 23 (from 19)

i'm new to varScan,i have the same issue....

[Jane M]

The last 4 columns are normal_reads1_plus normal_reads1_minus normal_reads2_plus normal_reads2_minus.

[SD2010Bioinfo]

The last 4 columns are normal_reads1_plus normal_reads1_minus normal_reads2_plus normal_reads2_minus.

Thank you for your reply. But in fact, you may not get the point.
The last 4 columns of the head is the content you mentioned. But the last 4 columns of variation informatin has extra 4 columns which has no corresponding head.

[Jane M]

Thank you for your reply. But in fact, you may not get the point.
The last 4 columns of the head is the content you mentioned. But the last 4 columns of variation informatin has extra 4 columns which has no corresponding head.

The last 4 columns of the head are tumor_reads1_plus tumor_reads1_minus tumor_reads2_plus tumor_reads2_minus, not normal_reads1_plus normal_reads1_minus normal_reads2_plus normal_reads2_minus.

If I understand well your question, you wonder what are the values 0 0 11 13 in the .snp file. Am I right?
In this case, these are normal_reads1_plus, normal_reads1_minus, normal_reads2_plus, normal_reads2_minus : 0+0=0 and 11+13=24 as in chr17 6115 G C 0 24.

[SD2010Bioinfo]

Sorry I misunderstood you.
I think your explanation is right to the question.
Thank you very much!

[dkoboldt]

I'm hereby promoting Jane M to "VarScan veteran". Thanks for the answers!

[Jane M]

Cool!
It's nice to answer and not to ask questions sometimes!