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.
