Combine samples in bam/vcf

Question

[vctrm67]

I have a single bam and vcf file that contains multiple sample names (as shown by bcftools query -l):

DS-bkm-116-N_TCCGTCTA_L001_R_001
DS-bkm-116-N_TCCGTCTA_L001_R_002
DS-bkm-116-N_TCCGTCTA_L001_R_003
DS-bkm-116-N_TCCGTCTA_L002_R_001
DS-bkm-116-N_TCCGTCTA_L002_R_002
DS-bkm-116-N_TCCGTCTA_L002_R_003
DS-bkm-116-N_TCCGTCTA_L003_R_001
DS-bkm-116-N_TCCGTCTA_L003_R_002
DS-bkm-116-N_TCCGTCTA_L003_R_003
DS-bkm-116-N_TCCGTCTA_L004_R_001
DS-bkm-116-N_TCCGTCTA_L004_R_002
DS-bkm-116-N_TCCGTCTA_L004_R_003
DS-bkm-116-N_TCCGTCTA_L005_R_001
DS-bkm-116-N_TCCGTCTA_L005_R_002
DS-bkm-116-N_TCCGTCTA_L005_R_003
DS-bkm-116-N_TCCGTCTA_L006_R_001
DS-bkm-116-N_TCCGTCTA_L006_R_002
DS-bkm-116-N_TCCGTCTA_L006_R_003
DS-bkm-116-T_ACACAGAA_L001_R_001
DS-bkm-116-T_ACACAGAA_L001_R_002
DS-bkm-116-T_ACACAGAA_L001_R_003
DS-bkm-116-T_ACACAGAA_L001_R_004
DS-bkm-116-T_ACACAGAA_L001_R_005
DS-bkm-116-T_ACACAGAA_L001_R_006
DS-bkm-116-T_ACACAGAA_L002_R_001
DS-bkm-116-T_ACACAGAA_L002_R_002
DS-bkm-116-T_ACACAGAA_L002_R_003
DS-bkm-116-T_ACACAGAA_L002_R_004
DS-bkm-116-T_ACACAGAA_L002_R_005
DS-bkm-116-T_ACACAGAA_L002_R_006
DS-bkm-116-T_ACACAGAA_L003_R_001
DS-bkm-116-T_ACACAGAA_L003_R_002
DS-bkm-116-T_ACACAGAA_L003_R_003
DS-bkm-116-T_ACACAGAA_L003_R_004
DS-bkm-116-T_ACACAGAA_L003_R_005
DS-bkm-116-T_ACACAGAA_L003_R_006
DS-bkm-116-T_ACACAGAA_L004_R_001
DS-bkm-116-T_ACACAGAA_L004_R_002
DS-bkm-116-T_ACACAGAA_L004_R_003
DS-bkm-116-T_ACACAGAA_L004_R_004
DS-bkm-116-T_ACACAGAA_L004_R_005
DS-bkm-116-T_ACACAGAA_L004_R_006
DS-bkm-116-T_ACACAGAA_L005_R_001
DS-bkm-116-T_ACACAGAA_L005_R_002
DS-bkm-116-T_ACACAGAA_L005_R_003
DS-bkm-116-T_ACACAGAA_L005_R_004
DS-bkm-116-T_ACACAGAA_L005_R_005
DS-bkm-116-T_ACACAGAA_L005_R_006
DS-bkm-116-T_ACACAGAA_L006_R_001
DS-bkm-116-T_ACACAGAA_L006_R_002
DS-bkm-116-T_ACACAGAA_L006_R_003
DS-bkm-116-T_ACACAGAA_L006_R_004
DS-bkm-116-T_ACACAGAA_L006_R_005
DS-bkm-116-T_ACACAGAA_L006_R_006

However, I believe this all corresponds to a single individual sample and these are just different lanes. Is there a way to combine these under a single sample name? Right now, I am having trouble running it through the GATK (which treats it as a multi-sample BAM) or using Annovar (which treats each as a separate sample).

Answer 1

[Pierre Lindenbaum]

a read group is set to a different sample name 'RG:SM' for each bam ( https://gatkforums.broadinstitute.org/gatk/discussion/6472/read-groups ) Use picard AddOrReplaceReadGroups http://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups to change the read groups of your bams.