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!
(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!
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