read starts with deletion. Cigar: 4D150M
Dear Sir,
I am using GATK v4.1.5.0 to call snp, the command is 'gatk --java-options " -Xmx32G " HaplotypeCaller --emit-ref-confidence GVCF -I CHR01_teFH2.bam -O CHR01.g.vcf -R CHR01.fa'. An error reported as 'A USER ERROR has occurred: Read A00262:316:HLW5MDSXX:3:1346:7844:3646 CHR01:1602331-1602484 is malformed: read starts with deletion. Cigar: 4D150M. Although the SAM spec technically permits such reads, this is often indicative of malformed files.'
The bam was got by bwa mem version: 0.7.17-r1188, and it passed the GATK ValidateSamFile check. I examined the bam and could not find the reads with a cigar '4D150M'. Again I rerun the command as 'gatk --java-options " -Xmx32G " HaplotypeCaller --read-filter GoodCigarReadFilter --emit-ref-confidence GVCF -I CHR01_teFH2.bam -O CHR01.g.vcf -R CHR01.fa', but the error still occurs.
Could you help me resolve it.
Thanks.
-
HI iOOv
This might be a bug and we are investigating it. You can follow the progress for this issue here: https://github.com/broadinstitute/gatk/issues/6490
To help us troubleshoot and fix this bug can you please share with us following:
- From the BAM file please share the problematic read with read name: Read A00262:316:HLW5MDSXX:3:1346:7844:3646 CHR01:1602331-1602484
- Please share with us the the input BAM as well
You can find instructions to share data here: https://gatk.zendesk.com/hc/en-us/articles/360035889671
-
Hi Bhanu Gandham!
I'm having the same problem with more than one sample. I've also tried with FixMateCigar but the problem remains.
"A USER ERROR has occurred: Read V300027291L3C003R0600645615 chr1:7026632-7026698 is malformed: read starts with deletion. Cigar: 3D64M36H. Although the SAM spec technically permits such reads, this is often indicative of malformed files.
A USER ERROR has occurred: Read V300027291L1C002R0370459277 chr9:17352390-17352461 is malformed: read starts with deletion. Cigar: 2D70M30H. Although the SAM spec technically permits such reads, this is often indicative of malformed files.
A USER ERROR has occurred: Read V300027195L4C005R0700962375 chr10:18036769-18036845 is malformed: read starts with deletion. Cigar: 20D57M43H. Although the SAM spec technically permits such reads, this is often indicative of malformed files.
..."
Denise
-
I am sorry that I have removed these files as I have successfully done the analysis by gatk 4.0.4.0. But I remember that there are reads mapped with large hard or soft clip as SUPPLEMENTARY mapping near the regions the reads with error report mapped. I hope this may helpful.
-
iOOv deni A bug fix is currently in code review: https://github.com/broadinstitute/gatk/pull/6498
Please sign in to leave a comment.
4 comments