Hi Folks,
this might seem like a naive quesiton, but please bear with me. Here is the output of two different varscan runs on a patient sample pre and post treatment.Each one is generated with seperate calls to mpileuptosnp, and are in different, single sample mpileup files. I am wondering why the consensus output (which is an amino acid code) is different for these samples when the variant allele is the same? In frame, both GAG and GAA should generate an E, not an R.
Chrom Position Ref Var Cons:Cov:Reads1:Reads2:Freq:P-value StrandFilter:R1+:R1-:R2+:R2-
val SamplesRef SamplesHet SamplesHom SamplesNC Cons:Cov:Reads1:Reads2:Freq:P-value
200-013-3_20_13_L7.LB2.snp:chr17 1631724 G A A:26:3:23:88.46%:7.3681E-12 Pass:3:0:12:11:1E0 0 0 1 0 A:26:3:23:88.46%:7.3681E-12
200-306-D1_L7.LB1.snp:chr17 1631724 G A R:24:11:13:54.17%:1.2938E-5 Pass:6:5:5:8:1E0 0 1 0 0 R:24:11:13:54.17%:1.2938E-5
Maybe I am not understanding the varscan mpileup2snp output completely.
this might seem like a naive quesiton, but please bear with me. Here is the output of two different varscan runs on a patient sample pre and post treatment.Each one is generated with seperate calls to mpileuptosnp, and are in different, single sample mpileup files. I am wondering why the consensus output (which is an amino acid code) is different for these samples when the variant allele is the same? In frame, both GAG and GAA should generate an E, not an R.
Chrom Position Ref Var Cons:Cov:Reads1:Reads2:Freq:P-value StrandFilter:R1+:R1-:R2+:R2-
val SamplesRef SamplesHet SamplesHom SamplesNC Cons:Cov:Reads1:Reads2:Freq:P-value200-013-3_20_13_L7.LB2.snp:chr17 1631724 G A A:26:3:23:88.46%:7.3681E-12 Pass:3:0:12:11:1E0 0 0 1 0 A:26:3:23:88.46%:7.3681E-12
200-306-D1_L7.LB1.snp:chr17 1631724 G A R:24:11:13:54.17%:1.2938E-5 Pass:6:5:5:8:1E0 0 1 0 0 R:24:11:13:54.17%:1.2938E-5
Maybe I am not understanding the varscan mpileup2snp output completely.