Gatk bam metrics

Question

[Sabeen]

Hello all,

I am trying to get bam file metrics and for this i am using gatk CollectAlignmentSummaryMetrics command. My code is as following

gatk CollectAlignmentSummaryMetrics -R hg19.fa -I RG.bam -O bammetrics.txt

my hg19.dict file is also in the same folder as the rest of the files mentioned above. I also created my dict file from unzipped reference file.

I am getting the error

SequenceUtil$SequenceListsDifferException: Sequences at index 1 don't match: 1/135534747/chr10 1/243199373/chr2/M5=a0d9851da00400dec1098a9255ac712e/UR=file:hg19.fa

Can any one please tell me what this error means and how to fix it.

Thanks in advance.

regards,
sabeen

[Pierre Lindenbaum]

the reference sequence that was used to map the reads is not the same as the one that you are using.

In the original REF the chromosomes were 1,2,3,4,5,6,7,8,9,10,11.... while this hg19 is 1,10,11,12,...

[Sabeen]

ok i get it thanks . but how do i fix it. also i want to mention that i used hg19 for the alignment of my file. ( what do you mean by original reference file)

[Pierre Lindenbaum]

what do you mean by original reference file

the reference file that was used to map the reads (with bwa or bowtie or etc... )

[Sabeen]

i used the same reference file for bwa alignment and here for CollectAlignmentSummaryMetrics