Question: Varscan Output Confusion
0
gravatar for rob234king
5.7 years ago by
rob234king580
UK/Harpenden/Rothamsted Research
rob234king580 wrote:

I'm performing SAMtools Mpileup using three samples followed by varscan:

samtools mpileup -E -C 50 -q 10 -f reference.fasta /home/data/bam/BWA_A_genome_P_trim15_75.sort.rmdup.bam /home/data/bam/cDNA/BWA_C_genome_P_trim15_75.sort.rmdup.bam /home/data/bam/cDNA/BWA_D_genome_P_trim15_75.sort.rmdup.bam > /home/data/SNP/BWA_A_C_D_P_trim15_75_C50q10.mpileup

java -jar /home/data/apps/VarScan.v2.3.4.jar mpileup2snp /home/data/SNP/BWA_A_C_D_P_trim15_75_C50q10.mpileup --min-coverage 5 --min-var-freq 0.01 --min-avg-qual 0 > /home/data/SNP/BWA_varscan_P_trim15_75_C50q10_Var_cov5_var0.01_Q0.out

Some of varscans output doesn't make sense to me. It is reporting a SNP but one, two, or all three samples final column report output like below:

Cons:Cov:Reads1:Reads2:Freq:P-value N:1:-:-:-:- N:3:-:-:-:- N:4:-:-:-:-

Chrom Position Ref Var Cons:Cov:Reads1:Reads2:Freq:P-value StrandFilter:R1+:R1-:R2+:R2-:pval SamplesRef SamplesHet SamplesHom SamplesNC Cons:Cov:Reads1:Reads2:Freq:P-value scaffold1 120 T C C:8:2:6:75%:3.4965E-3 Pass:0:0:0:0:1E0 0 0 0 3 N:1:-:-:-:- N:3:-:-:-:- N:4:-:-:-:-

I assumed that these positions had only N's present but checking using tablet and they have SNP's and the reference is not N's either so why are the last columns data not populated with numbers?

Maybe I'm just confused by what the columns mean, The SamplesNC column means: Number of samples not covered / not called

so not calling them because.....maybe p value is not set, so should be default 99e-02 but program says "no p--value not provided so will not be calculated" but output of settings says 0.01 is set p-value? changing it to include the parameter with the default value still results in these no calls.

varscan • 2.7k views
ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by rob234king580
1
gravatar for rob234king
5.7 years ago by
rob234king580
UK/Harpenden/Rothamsted Research
rob234king580 wrote:

Solved my own problem, just a matter of setting the coverage if want to call these non-calls as it is a coverage factor. There does seem to be a bug for the p-value though, this needs to be set because the default is not working.

ADD COMMENTlink written 5.7 years ago by rob234king580
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