We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

GATK4 SplitNCigarReads: file size of bam file is "0"

hi, I run the following command lines for my RNA_Seq data, no error showed, but part of the samples after "SplitNCigarReads", the file size of split.bam files were "0", could you please help to check ?

the command line is:
~gatk SplitNCigarReads \
-R ${reference} \
-I ${outputdir}/~/${SM}.dedupped.bam \
-O ${outputdir}/~/${SM}.split.bam \
-RMQF 255 \
-RMQT 60 \
-U ALLOW_N_CIGAR_READS

Answers

Sign In or Register to comment.