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dkoboldt / varscan

Variant calling and somatic mutation/CNV detection for next-generation sequencing data
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VCF format problem VarScan2.41.0 #8

Open mortunco opened 8 years ago

mortunco commented 8 years ago

Hi,

I ran the following code but output was in VarScan format.

TuncBook-Pro:blackhole morova$ java -jar ~/varscan/VarScan.v2.4.1.jar somatic normal/normal.mpileup tumor/tumor.mpileup --output-vcf 1

This is my header info from the output of the following command. 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

Please help me,

Best,

Tunc

nanakiksc commented 6 years ago

If you want VCF output, make sure you are using mpileup2(snp|indel|cns) instead of pileup2(snp|indel|cns).