Varuni Sarwal

Hi, I tried to run Varscan using the command java -jar -Xmx12M $toolPath pileup2indel. The output format is the following: Chrom Position Ref Cons Reads1 Reads2 VarFreq Strands1 Strands2 Qual1 Qual2 Pvalue MapQual1 MapQual2 Reads1Plus Reads1Minus Reads2Plus Reads2Minus VarAllele 19 3001225 C /-AGTGCATT 20 3 13.04% 2 2 37 20 0.98 1 1 8 12 1 2 -AGTGCATT 19 3001628 C /+AGT 17 3 14.29% 2 2 34 29 0.98 1 1 9 8 2 1 +AGT 19 3002263 G */-TT 29 2 6.45% 2 1 37 37 0.98 1 1 12 17 0 2 How can I calculate the end...

When i run Scalpel on sample data, I get the following error. I am using a bed file of the format chromosome_number:start-end Loading targets from BED file...Use of uninitialized value $chr in string eq at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/SequenceIO.pm line 209, <EXONSLIST> line 2. Use of uninitialized value in hash element at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/SequenceIO.pm line 224, <EXONSLIST> line 2. Use of uninitialized value in string eq at /u/home/v/vsarwal/codes/Scalpel/scalpel-0.5.3/SequenceIO.pm...