Entering edit mode
7.2 years ago
human_genomeXXX
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10
How to to run GATK variant call on the .bam or .sam and reference in a minimal lines of code?
I have the output from the BWA and nit to call variants with GATK. Not clear in details from the documentation.
That's a very lazy question, while the documentation of GATK is very clear.
Have you read the GATK documentation?
If you are concerned with speed, the best choice is to call variants with the BBMap package:
thank you, but how to specify Xmxm for BBmap when there is an error?
You probably should be more specific
in other words, how to input 2 fastqs (?) in= 0001.fastq, 0002.fastq do not work
thank you
You mean for mapping? Be more specific. Read the manual.
Like you have technical replicates that you want merged into one BAM, or different samples, or oddly named paired-end reads, or...
Are you intentionally trying to make it difficult for people to help you?
You can't call variants from fastq files... you need to map the reads first.
The correct syntax for specifying multiple files is:
If you have trouble with memory, you can add the flag "-Xmx20g" or something like that, which specifies how many GB of RAM to use. If you run out of memory, you can reduce the memory consumption with the "prefilter" flag. Also, if this is human data, you should add the flag "ploidy=2".
thank you ++++++++++++++
how to input two reads.fastq? not one...
Read The Fantastic Manual
And, by the way, what tools can annotate output from BBMap besides SNPEff, thanks