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bam is malformed depthofcoverage

remimaglioneremimaglione Posts: 3Member
edited May 2013 in Ask the GATK team

Hello,

i have spend many hours trying to run GATK depthofcoverage but it never works.
last try: -T DepthOfCoverage -R /home/remi/Analyse/CNV/ERR125905/bam/Chloroplastgenomebarley.fa -I /home/remi/Analyse/CNV/ERR125905/bam/ERfiltre.bam -L /home/remi/Analyse/CNV/ERR125905/bam/ERfiltre.bed -o /home/remi/Analyse/CNV/FishingCNV_1.5.3/out/ERfiltre.bam.coverage --minMappingQuality 15 --minBaseQuality 10 --omitDepthOutputAtEachBase --logging_level INFO --summaryCoverageThreshold 5 --summaryCoverageThreshold 7 --summaryCoverageThreshold 10 --summaryCoverageThreshold 15 --summaryCoverageThreshold 20 --summaryCoverageThreshold 30 --summaryCoverageThreshold 50

My BAM header seem to be malformed.

ERROR MESSAGE: SAM/BAM file /home/remi/Analyse/CNV/ERR125905/bam/ERfiltre.bam is malformed: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups

here is the 1rst line of the header:

`@SQ SN:Chloroplastgenomebarley LN:136462

@PG ID:bwa PN:bwa VN:0.5.9-r16
ERR125905.35 99 Chloroplastgenomebarley 69543 29 101M = 69854 412 TTTGATCCCTCTGATCCTGTTCTGGATCCAATGTGGAGACAAGGTATGTTCGTAATTCCCTTCATGACTCGTTTAGGAATAACGGATCCTTGGGGTGGTTG D-:D?BDDDDCC-?ADCBBBDDDDD:BDD= :6 C-4<9@62@@<;:?=B??B=DC28=B&?:AA:4
@ 66DD@-@DDD?B::@-CA:5?:ADD?ADBB??`

I Have search in the forum and doc about it. I have try to reorder my header with picard:

`@HD VN:1.4 SO:unsorted

@SQ SN:Chloroplastgenomebarley LN:136462 UR:file:/home/remi/Analyse/REFGEN/Chloroplastgenomebarley.fa M5:7a7b36ef01cc1a2af1c8451ca3800f93
@PG ID:bwa PN:bwa VN:0.5.9-r16
ERR125905.35 99 Chloroplastgenomebarley 69543 29 101M = 69854 412 TTTGATCCCTCTGATCCTGTTCTGGATCCAATGTGGAGACAAGGTATGTTCGTAATTCCCTTCATGACTCGTTTAGGAATAACGGATCCTTGGGGTGGTTG D-:D?BDDDDCC-?ADCBBBDDDDD:BDD= :6 C-4<9@62@@<;:?=B??B=DC28=B&?:AA:4
@ 66DD@-@DDD?B::@-CA:5?:ADD?ADBB??
`
but no more change.

Someone can help me please ?

Regards,
Remi

`

Answers

  • CarneiroCarneiro Posts: 274Administrator, Dev admin

    You need to add a read group tag to your BAM to use it with the GATK. During BWA alignment (which you're using a very old version, btw) you could have added it with the -R option. Now you can still use Picard Tools to add a read group to your bam file. Without a Read Group tag, no GATK tool will run on your bam.

  • remimaglioneremimaglione Posts: 3Member

    thank you for your reply,
    you're right, I did not use the-R option on my alignment with BWA.
    I'll go back on it later to tell you if all goes well.

  • remimaglioneremimaglione Posts: 3Member
    edited May 2013

    After a new alignment, i have had manualy the header with picard tools in my SAM (after read filter and before SAM to BAM conversion). I have try a CountRead in order to test if GATK can run my new BAM... and it works FINE. I will try to do a depthOfcoverage and tell later if all goes well.

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