GATK_SplitNCigarReads output size is empty

Question

[JackShao]

Hi, I am a new for NGS. It is my first time to run RNAseq analysis to find mutation with GATK4. I get bam files after I made alignment with STAR software. Then, I remove duplicates using sambamba: sambamba markdup --overflow-list-size 600000 --tmpdir='./' -r M137192_sorted.bam M137192_sorted_rmdup.bam After that, I do GATK4 to get the split bam file: gatk --java-options "-Xmx20G -Djava.io.tmpdir=./" SplitNCigarReads -R /fdb/GATK_resource_bundle/hg38/Homo_sapiens_assembly38.fasta -I M137192_rmdup.bam -O M137192_rmdup_split.bam

There is no error in log, but the output is empty: $ du -h M137192_sort_rmdup_split.bam 0 M137192_sort_rmdup_split.bam

I am confused and who has any ideas about this problem? Thank you in advance.

Best and happy Thanksgiving

Answer 1

[JackShao]

I have figured it out. Just using GATK3 version to do SplitNCigarRead, and get the split.bam, then go back to GATK4 pipeline.