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Tag: MarkduplicatesSpark
GATK not working when clone to VM
GATK not working when clone to VM 0 I has successfully installed gatk for a long time on my computer. Now I got a workstation and cloning it to ubuntu server VM. However, when run the testing with MarkDuplicatesSpark it does not worked like on my computer. This is the…
Detailed differences between sambamba and samtools
3 month , My first post in the new student group , The false-positive mutation appears because duplicates mark Not enough ?, Tells the story of supplementary read It won’t be GATK MarkDuplicates Marked as duplicates The problem of . after , In response to this question , I began…
sequence alignment – MarkDuplicatesSpark failing with cryptic error message. MarkDuplicates succeeds
[*] I have been trying to follow the GATK Best Practice Workflow for ‘Data pre-processing for variant discovery’ (gatk.broadinstitute.org/hc/en-us/articles/360035535912). This has all been run on Windows Subsystem for Linux 2 on the Bash shell. I started off with FASTQ files from IGSR (www.internationalgenome.org/data-portal) and performed alignment with Bowtie2 (instead of…
MarkduplicatesSpark How to speed-up ?
MarkduplicatesSpark How to speed-up ? 0 Hello all, I would like to know if there is any good option to speed up MarkduplicatesSpark ? I work with human genome with arround 900 millions reads (151 bp). I work on a cluster (with slurm). The command that i used is (with…
So many variants detected.
So many variants detected. 0 Dear All, I have done variant calling in Germline data that has single sample of each individual and two genes. I did following steps, but after checking results I found too many variants. After Haplotypecaller (the step 6) I found 140900 known variants, and the…