We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
question about MergeBamAlignment
I am trying to use the pipeline from the best practice to analysis some exome data. But I get confused on the step "MergeBamAlignment".
We used bwa to map the fastq file to the reference and then, generated unmapped bam file using picard. After we merged the aligned bam file (A) and unmapped file (B), we got a merged bam file(C). However, the merge file (C) has a smaller size than both A and B.
5.7G sample.raw.bam (B)
According to informations from the guidance that MergeBamAlignment takes metadata from a SAM or BAM file of unmapped reads (uBAM) and merges it with a SAM or BAM file containing alignment records for a subset of those reads, i thought the merged file would be the largest file in A, B, and C.(http://gatkforums.broadinstitute.org/gatk/discussion/5969/how-to-generate-a-bam-for-variant-discovery-long#step7)
Why the merged file is smaller than others?
Here is my command:
$bwa mem -t 12 \
-R "@RG\tID:ID001\tLB:sample001\tSM:sample001\tPL:ILLUMINA" \
$data_dir/sample001/ID001_1.clean.fq.gz $data_dir/sample001/ID001_2.clean.fq.gz > $sam_dir/ID001.aligned.sam
java -jar $picard/SortSam.jar \
generate unmapped bam file
java -jar $picard/FastqToSam.jar \
merge two bam file
java -jar $picard/MergeBamAlignment.jar \
I would be very grateful of any advice!