Dear All,

I was trying to usedeep SNV to analyze exome-seq data.

I encountered a problem while a specific exon counts are all zero. when I check the read coverage with igv it clearly shows that the exon is covered with multiple reads.

Since my region of interest is TP53, I use bam2R to extract counts of this region chr17:7571719-7571719. Igv shows more than 1000 reads in this region with a coverage of 1156 at position 7578115.

while using BAM2R:

bam2R("H:\\NH150496\\Results\\Bam\\P1195_cancer.final.bam", "17", 7578115, 7578116, q = 25, s = 2, head.clip = 0,max.depth = 1e+06, verbose = FALSE)

the output shows:

===============================================================================

 A T C G - N INS DEL HEAD TAIL QUAL a t c g _ n ins del head tail qual
[1,] 0 0 0 0 0 0   0   0    0    0    0 0 0 0 0 0 0   0   0    0    0    0
[2,] 0 0 0 0 0 0   0   0    0    0    0 0 0 0 0 0 0   0   0    0    0    0

================================================================================

which is all zero.

I used hg19 as reference genome.

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I somehow solve this problem by using another system. It seems that windows can not properly process deepSNV compared to ubuntu.