zhongwulai
commented
9 years ago Li Tai,
It might be the same problem that we discussed, where a read is aligned in a stretch of Ns. Can you check whether it's the case? You can send BAM files through email. 1.5 MB should be OK.
Thanks, Zhongwu
I have seen the following exit message on error:
Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: -1 at java.lang.String.charAt(String.java:658) at com.astrazeneca.vardict.VarDict.modifyCigar(VarDict.java:6065) at com.astrazeneca.vardict.VarDict.parseSAM(VarDict.java:1529) at com.astrazeneca.vardict.VarDict.toVars(VarDict.java:2515) at com.astrazeneca.vardict.VarDict.somaticNotParallel(VarDict.java:356) at com.astrazeneca.vardict.VarDict.nonAmpVardict(VarDict.java:251) at com.astrazeneca.vardict.VarDict.start(VarDict.java:67) at com.astrazeneca.vardict.Main.run(Main.java:137) at com.astrazeneca.vardict.Main.main(Main.java:24)
I have two small BAM files of 1.5 MB each in size that can reproduce this error.
Command used were: VarDictJava/build/install/VarDict/bin/VarDict -G human_g1k_v37_decoy.fasta -f 0.01 -h -b 'tumor.errored.bam|normal.errored.bam' -C -c 1 -S 2 -E 3 -g 4 errored.5kbps.bed 2> errored.msg > errored.var
Is there a way I can get the BAM files to you guys?
Thanks.