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Old 10-31-2014, 01:12 AM   #1
balthasar
Junior Member
 
Location: Germany

Join Date: Oct 2014
Posts: 5
Default problems with varscan2.3.7

hi,

i am using varscan in the following command for germline/somatic calls:

samtools mpileup -q 20 -Q 20 -f hg19.fa -B file_norm file_tum | varscan_somatic - outname --mpileup 1 --strand-filter 1 --min-coverage-normal 10 --min-coverage-tumor 10 --min-var-freq 0.08 --p-value 0.05

samtools version is 1.1.

1.
i am getting variants like this one:

1 809876 A G 8 12 60% R 2 6 75% G Germline 6.18058411139014E-8 0.38524374176547704 0 2 0 6 0 8 0 12
(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 normal_reads1_plus normal_reads1_minus normal_reads2_plus normal_reads2_minus)

so, if i am not mistaken, --min-coverage-tumor has been violated. why???

2.
also, i am getting:

1 871334 G T 0 11 100% T 0 11 100% T Germline 4.75262816646234E-013 1 0 0 0 11 0 0 0 11
(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 normal_reads1_plus normal_reads1_minus normal_reads2_plus normal_reads2_minus)

so, strand bias is maximally violated, isnt it? but why???

maybe, i dont see the simple things but any help would be very appreciated!

thanks, chris
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coverage filter, somatic, strand filter, varscan

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