Gatk bam metrics
0
0
Entering edit mode
19 days ago
Sabeen • 0

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

ngs metrics bam Gatk • 230 views
ADD COMMENT
0
Entering edit mode

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,...

ADD REPLY
0
Entering edit mode

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)

ADD REPLY
0
Entering edit mode

what do you mean by original reference file

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1471 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6