You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Could you help me direct to preparing input files for running pyclone from snp output of VarScan?
Here is the content of a snp file.
Native header | VCF field name | Description
chrom | CHROM | Chromosome or reference name
position | POS | Position from SAMtools pileup (1-based)
ref | REF | Reference base at this position
var | ALT | Variant base seen in tumor
normal_reads1 | RD (col 10) | Reads supporting reference in normal
normal_reads2 | AD (col 10) | Reads supporting variant in normal
normal_var_freq | FREQ (col 10) | Variant allele frequency in normal
normal_gt | GT (col 10) | Consensus genotype call in normal
tumor_reads1 | RD (col 11) | Reads supporting reference in tumor
tumor_reads2 | AD (col 11) | Reads supporting variant in tumor
tumor_var_freq | FREQ (col 11) | Variant allele frequency in tumor
tumor_gt | GT (col 11) | Consensus genotype in tumor
somatic_status | SS (col 8) | Somatic status (Germline, Somatic, LOH, Unknown)
variant_p_value | GPV (col 8) | Variant p-value from FET for germline events (tumor + normal vs reference)
somatic_p_value | SPV (col 8) | Somatic p-value from FET (tumor vs normal)
tumor_reads1_plus | DP4 (col 11) | Tumor reference-supporting reads on + strand
tumor_reads1_minus | | Tumor reference-supporting reads on – strand
tumor_reads2_plus | | Tumor variant-supporting reads on + strand
tumor_reads2_minus | | Tumor variant-supporting reads on - strand
normal_reads1_plus | DP4 (col 10) | Normal reference-supporting reads on + strand
normal_reads1_minus | | Normal reference-supporting reads on – strand
normal_reads2_plus | | Normal variant-supporting reads on + strand
normal_reads2_minus | | Normal variant-supporting reads on - strand
The text was updated successfully, but these errors were encountered:
Hello Dear Roth,
Could you help me direct to preparing input files for running pyclone from snp output of VarScan?
Here is the content of a snp file.
Native header | VCF field name | Description
chrom | CHROM | Chromosome or reference name
position | POS | Position from SAMtools pileup (1-based)
ref | REF | Reference base at this position
var | ALT | Variant base seen in tumor
normal_reads1 | RD (col 10) | Reads supporting reference in normal
normal_reads2 | AD (col 10) | Reads supporting variant in normal
normal_var_freq | FREQ (col 10) | Variant allele frequency in normal
normal_gt | GT (col 10) | Consensus genotype call in normal
tumor_reads1 | RD (col 11) | Reads supporting reference in tumor
tumor_reads2 | AD (col 11) | Reads supporting variant in tumor
tumor_var_freq | FREQ (col 11) | Variant allele frequency in tumor
tumor_gt | GT (col 11) | Consensus genotype in tumor
somatic_status | SS (col 8) | Somatic status (Germline, Somatic, LOH, Unknown)
variant_p_value | GPV (col 8) | Variant p-value from FET for germline events (tumor + normal vs reference)
somatic_p_value | SPV (col 8) | Somatic p-value from FET (tumor vs normal)
tumor_reads1_plus | DP4 (col 11) | Tumor reference-supporting reads on + strand
tumor_reads1_minus | | Tumor reference-supporting reads on – strand
tumor_reads2_plus | | Tumor variant-supporting reads on + strand
tumor_reads2_minus | | Tumor variant-supporting reads on - strand
normal_reads1_plus | DP4 (col 10) | Normal reference-supporting reads on + strand
normal_reads1_minus | | Normal reference-supporting reads on – strand
normal_reads2_plus | | Normal variant-supporting reads on + strand
normal_reads2_minus | | Normal variant-supporting reads on - strand
The text was updated successfully, but these errors were encountered: