Dan, thank you a lot for your detailed answer.
1) I would like to come back to the Min-Reads2 and Min-Strands2 parameters.
I understand why they are used for, but I'm wondering what is happening in some cases, for example:
Since there is no variant in the tumor samples, if we use Min-Reads2>0, the position won't be considered as "LOH", whereas it is, am I right?
2) Then, I would like to know if VarScan could be use to compare 2 tumor samples. For several patients, I have a normal sample, an untreated sample and a treated sample.
I want to study the effect of the treatment.
I am comparing normal/untreated (1), normal/treated (2) and finally (1) vs (2). But it would be much faster to directly compare untreated/treated. I am wondering if there is something which prevents to do so in VarScan. What do you think ?
3) Finally, for the issue concerning the number of reads in .indel file, here are 2 postions:
Varscan output:
Mpileup output:
Thank you for your help,
Jane
1) I would like to come back to the Min-Reads2 and Min-Strands2 parameters.
Originally posted by dkoboldt
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- 50 (reference in normal sample) 50 (variant in normal sample) 100 (reference in tumor sample) 0 (variant in tumoral sample)
- 0 (reference in normal sample) 100 (variant in normal sample) 100 (reference in tumor sample) 0 (variant in tumoral sample)
Since there is no variant in the tumor samples, if we use Min-Reads2>0, the position won't be considered as "LOH", whereas it is, am I right?
2) Then, I would like to know if VarScan could be use to compare 2 tumor samples. For several patients, I have a normal sample, an untreated sample and a treated sample.
I want to study the effect of the treatment.
I am comparing normal/untreated (1), normal/treated (2) and finally (1) vs (2). But it would be much faster to directly compare untreated/treated. I am wondering if there is something which prevents to do so in VarScan. What do you think ?
3) Finally, for the issue concerning the number of reads in .indel file, here are 2 postions:
Varscan output:
Code:
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 chr1 20098 C -AG 10 0 0% C 6 2 25% */-AG Somatic 1.0 0.1830065359477151 7 1 1 1 chr1 3418647 G -C 16 0 0% G 7 5 41,67% */-C Somatic 1.0 0.008058608058608 4 6 4 1
Code:
$ grep -w 20098 fibros.mpileup chr1 20098 c 10 .$..,,,.,., EJJIH?EEDD $ grep -w 20098 tumor.mpileup chr1 20098 c 8 ....-2AG.,-2ag.. JJIEJEHF
Jane
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