Hi everyone,

I used bwa to index my reference genome: bwa index ref_genome.fna.gz

I used bwa mem command on my paired end genome assembly:

the command: bwa mem -t 10 ref_genome.fna.gz FISH_DATA/Individuals/F1/F1_1.fq.gz /FISH_DATA/Individuals/F1/F1_2.fq.gz > f1_map2ref.sam

convert sam to bam: samtools view -S -b -t 10 f1_map2ref.sam > f1_map2ref.bam

then I sorted: samtools sort -o f1_map2ref.sorted.bam f1_map2ref.bam

then I used picard ValidateSamFile on the output (after mapping my assembly to the ref genome convert to bam and sort)

the command:

java -jar picard.jar ValidateSamFile \ -I f1_map2ref.sorted.bam -MODE SUMMARY

The results: ## HISTOGRAM java.lang.String Error Type Count ERROR:MISSING_READ_GROUP 1 WARNING:RECORD_MISSING_READ_GROUP 499577401

I would be very grateful if anyone would help me understand how to fix the problem

Hi Michal, this question is not related to any R / Bioconductor package; therefore, you should instead post it at Biostars or Bioinformatics Stack Exchange.

Thanks,

Kevin

PS - you can probably solve the issue by adding a read group to your BAM file. Please take a look at: https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrReplaceReadGroups-Picard-

Either that, or you can add the read group during alignment via the -R command line parameter that is passed to bwa mem:

-R STR        read group header line such as '@RG\tID:foo\tSM:bar' [null]