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AddOrReplaceReadGroups in picard

AddOrReplaceReadGroups in picard is unavailable for the reference sequence with large chromosomes (500 Mbp). I wanted to call SNPs using the reference sequence with large chromosomes. But I could not use mpileup or unifiedgenotype in GATK without AddOrReplaceReadGroups. Are there any methods of SNP call without AddOrReplaceReadGroups?

genome snp sequencing
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by ago1mutant • ago1mutant

don't waste your time: GATK is like picard is based on htsjdk library which cannot work with large contig (> INT_MAX) too

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written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

you can always add a group using awk:

samtools view -h your.bam |\
awk '/^@HD/ {print;printf("@RG\tID:SAMPLE1\tSM:SAMPLE1\n"); next;} {printf("%s\tRG:Z:SAMPLE1\n",$0);}' |\
samtools view -S -b -o rg.bam -
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written by Pierre Lindenbaum Pierre Lindenbaum

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