Hello,
I'm aware this issue (or similar) has been alerady posted but I don't get DINDEL to work for the 'Stage 3' (version 1.0, page 4 of the documentation). Basically it asks me for the candiate variant file ('Please specify the file with the candidate variants.'). However I think I've already supplied the windows file using the following command where '--varFile' is used for that.
[PATH_TO_DINDEL]/dindel \
--analysis indels \
--doDiploid \
--bamFile [PATH_TO_BAM_FILE]/file.bam \
--ref [PATH_TO_REFERENCE_GENOME]/hg19.fa \
--varFile [PATH_TO_CANDIDATE_VARIANTS_FILE]/file.windows.1.txt \
--libFile [PATH_TO_LIBRARY_FILE]/file.libraries.txt \
--outputFile [PATH_FOR_OUTPUT_FILE]
I would d be grateful if someone could help me to identify what I'm dowing wrong.
Thanks a lot
Jorge
I'm aware this issue (or similar) has been alerady posted but I don't get DINDEL to work for the 'Stage 3' (version 1.0, page 4 of the documentation). Basically it asks me for the candiate variant file ('Please specify the file with the candidate variants.'). However I think I've already supplied the windows file using the following command where '--varFile' is used for that.
[PATH_TO_DINDEL]/dindel \
--analysis indels \
--doDiploid \
--bamFile [PATH_TO_BAM_FILE]/file.bam \
--ref [PATH_TO_REFERENCE_GENOME]/hg19.fa \
--varFile [PATH_TO_CANDIDATE_VARIANTS_FILE]/file.windows.1.txt \
--libFile [PATH_TO_LIBRARY_FILE]/file.libraries.txt \
--outputFile [PATH_FOR_OUTPUT_FILE]
I would d be grateful if someone could help me to identify what I'm dowing wrong.
Thanks a lot
Jorge
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