#gatk — Public Fediverse posts

I asked #biostars : "Parabricks : Number of GPUs requested (2) is more than number of GPUs (0) in the system., exiting."
https://www.biostars.org/p/9614740/

#bioinformatics #parabricks #NVIDIA #haplotypecaller #gatk #gpus

TIL: You can get a list of Spark-enabled GATK tools with the command

gatk --list | grep Spark

(The website doesn't seem to have a list anywhere)

#bioinformatics #GATK #ApacheSpark

I was given a BAM. I see the following tags in the SAM:

'de:f:0.0067 rl:i:0 cm:i:19 nn:i:0 tp:A:P ms:i:288'

#GATK HaplotypeCaller crashed because of those tags. ( https://gatk.broadinstitute.org/hc/en-us/community/posts/11440622639387-Unable-to-trim-uncertain-bases-without-flow-order-information )

The only tools used (header/@PG) are bwa: 7.15-r1142-dirty and MarkDuplicates.
which tool added those tags ?

#sam #bam #bwa

https://www.nature.com/articles/s41598-022-26181-3 "Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment" #gatk #dragen #deepvariant #genomics #wgs

I've have the feeling that the #VCF called by ILMN / #dragen and #gatk are quite different. 🤔