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Piped command for realignment of BAM files

jushjush PhillyMember
Sorry for any errors, I'm new to the forum

I'm currently trying to realign my bam file to the hg38 reference genome. I tried my own piped command and also the command from GATK tutorial 6483

gatk SamToFastq -I markedadapters.bam -F /dev/stdout --CLIPPING_ATTRIBUTE XT --CLIPPING_ACTION 2 --INTERLEAVE true -NON_PF true -TMP_DIR= path/hello | bwa mem -M -t 12 -p /mydata/Homo_sapiens_assembly38.fasta /dev/stdin | gatk MergeBamAlignment --ALIGNED_BAM /dev/stdin --UNMAPPED_BAM unmap.bam -O piped.bam -R /mydata/Homo_sapiens_assembly38.fasta --CREATE_INDEX true --ADD_MATE_CIGAR true --CLIP_ADAPTERS false --CLIP_OVERLAPPING_READS true --INCLUDE_SECONDARY_ALIGNMENTS true --MAX_INSERTIONS_OR_DELETIONS -1 --PRIMARY_ALIGNMENT_STRATEGY MostDistant --ATTRIBUTES_TO_RETAIN XS -TMP_DIR= path/hello

but I kept getting this error:

htsjdk.samtools.SAMException: Error in writing fastq file /dev/stdout

I ran SamToFastq by itself in this format and it worked

gatk SamToFastq -I markedadapters.bam -F /dev/stdout --CLIPPING_ATTRIBUTE XT --CLIPPING_ACTION 2 --INTERLEAVE true -NON_PF true -TMP_DIR= path/hello > mytest.fastq

I'd love to be able to use piped commands since my bam files are 150G


  • bshifawbshifaw Member, Broadie, Moderator admin


    If you see the following [E::bwa_idx_load_from_disk] fail to locate the index files Try indexing your fasta with bwa then run your command again. Forum post

    bwa index Homo_sapiens_assembly38.fasta 

    If not please post the full stacktrace for running your command to this thread.

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