Hi Dan, I run varScan twice on same mpileup iinput file. In somatic mode it works but in copynumber it chokes with:
Reading mpileup input... Parsing Exception on line: chr1 14143 C 0 * * 0 8
First of all, java should have exited with a non-zero return value. I started it with 'java -jar ... || exit 255'.
Second, I do not know where the number 8 comes from in the above output.
Below is the mpileup file content at about that line.
chr1 14140 G 0 * * 1 . @ chr1 14141 G 0 * * 1 . A chr1 14142 G 0 * * 1 . A chr1 14143 C 0 * * 0 chr1 14144 C 0 * * 1 . ; chr1 14145 A 0 * * 1 . @ chr1 14146 T 0 * * 1 . =
I see to remember from other threads there was an issue with zero coverage lines ... maybe still unfixed in copynumber mode?
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Hi Dan,
I run varScan twice on same mpileup iinput file. In somatic mode it works but in copynumber it chokes with:
First of all, java should have exited with a non-zero return value. I started it with 'java -jar ... || exit 255'.
Second, I do not know where the number 8 comes from in the above output.
Below is the mpileup file content at about that line.
I see to remember from other threads there was an issue with zero coverage lines ... maybe still unfixed in copynumber mode?