the bug about argument "--ignoreRG"

[WortJohn]

Hi, I have tumor_1.bam and matched normal_1.bam. When i execute the VerifyBamID program, i get the right result. And the log records the information "Total of 1 out of 1 individuals successfully matched IDs". The information of selfSM file is as follow:

#SEQ_ID RG CHIP_ID #SNPS #READS AVG_DP FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF RDPHET RDPALT 11T0043364AP1 ALL 11T0043364AP1 227 4524 19.93 0.09733 2351.23 2464.59 NA NA 0.55276 2289.24 2308.96 NA NA -nan -nan -nan

But when I rename tumor_1.bam as tumor_2.bam and normal_1.bam as normal_2.bam and execute the VerifyBamID program with "--ignoreRG" argument, i get the wrong result. And the log records the information "Total of 0 out of 1 individuals successfully matched IDs". The information of selfSM file is as follow:

#SEQ_ID RG CHIP_ID #SNPS #READS AVG_DP FREEMIX FREELK1 FREELK0 FREE_RH FREE_RA CHIPMIX CHIPLK1 CHIPLK0 CHIP_RH CHIP_RA DPREF RDPHET RDPALT 11T0043364AP1 ALL NA 227 4524 19.93 0.09733 2351.23 2464.59 NA NA NA NA NA NA NA NA NA NA

Supplementary information:

I use verifyBamID 1.1.3 and the command is as follow:

/public/biowork/tool/software/miniconda3/envs/py368/bin/verifyBamID
--vcf /public/biowork/seq_data/current/230408_NDX550741_A/verifyBamID/11T0043364AB1.af.vcf
--bam /public/biowork/seq_data/current/230408_NDX550741_A/BAM/11T0043364AB1.dedup.bam
--out /public/biowork/seq_data/current/230408_NDX550741_A/verifyBamID/11T0043364AB1
--ignoreRG

/public/biowork/tool/software/miniconda3/envs/py368/bin/verifyBamID
--vcf /public/biowork/seq_data/current/230408_NDX550741_A/verifyBamID/11T0043364AP1.af.vcf
--bam /public/biowork/seq_data/current/230408_NDX550741_A/BAM/11T0043364AP1.dedup.bam
--out /public/biowork/seq_data/current/230408_NDX550741_A/verifyBamID/11T0043364AP1
--ignoreRG

[Griffan]

Hi, did you mix tumor bam and normal bam into the same bam file? and how many read groups are there in your sequencing data?

[WortJohn]

I did not mix bam file and only renamed the file name. The bam file had only one read group. It was just like that i renamed "A.bam" as "B.bam". The RG information was still "@ RG ID:A PL:Illumina LB:A SM:A PG:bwa" in header and "RG:Z:A" in each alignment record for "B.bam".

[Griffan]

Could you provide the related bam header information?