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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 ERR125905.35 147 Chloroplastgenomebarley 69854 29 101M = 69543 -412 GGCTTTCTGTCGCTTGTGGGCTTTTCCTATAACGGCTTTTTATGTTCCTGGGATATGGGTATCCGATCCTTATGGACTAACTGGAAAAGTACAAGCTGTAA #################################################A-B49= @@2>+:CCC:@@ 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 ERR125905.35 147 Chloroplastgenomebarley 69854 29 101M = 69543 -412 GGCTTTCTGTCGCTTGTGGGCTTTTCCTATAACGGCTTTTTATGTTCCTGGGATATGGGTATCCGATCCTTATGGACTAACTGGAAAAGTACAAGCTGTAA #################################################A-B49= @@2>+:CCC:@@ 66DD@-@DDD?B::@-CA:5?:ADD?ADBB?? but no more change.

Someone can help me please ?

Regards, Remi

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