Check on "m2_extra_args", "m2_extra_filtering_args" used in mitochondria pipeline
AnsweredHi GATK team,
I'm exploring on the mitochondrial pipeline.
In particular, at the step of using MuTect2 at CallMT step (see also AlignAndCall wdl), I noticed "m2_extra_args" are being used but could not find further information about it.
gatk --java-options "-Xmx~{command_mem}m" Mutect2 \ -R ~{ref_fasta} \ -I ~{input_bam} \ --read-filter MateOnSameContigOrNoMappedMateReadFilter \ --read-filter MateUnmappedAndUnmappedReadFilter \ -O ~{output_vcf} \ ~{true='--bam-output bamout.bam' false='' make_bamout} \ ~{m2_extra_args} \ --annotation StrandBiasBySample \ --mitochondria-mode \ --max-reads-per-alignment-start ~{max_reads_per_alignment_start_arg} \ --max-mnp-distance 0
As well as for "m2_extra_filtering_args", at the Filter step.
gatk --java-options "-Xmx2500m" FilterMutectCalls -V ~{raw_vcf} \ -R ~{ref_fasta} \ -O filtered.vcf \ --stats ~{raw_vcf_stats} \ ~{m2_extra_filtering_args} \ --max-alt-allele-count ~{max_alt_allele_count} \ --mitochondria-mode \ ~{"--min-allele-fraction " + vaf_filter_threshold} \ ~{"--f-score-beta " + f_score_beta} \ ~{"--contamination-estimate " + max_contamination}
Wondering what were the "m2_extra_args" and "m2_extra_filtering_args" used for the mitochondrial pipeline?
Thank you so much.
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Thank you for your post, Michelle Lian! I want to let you know we have received your question and will be moving it to the Community Discussions -> General Discussion topic, as the Other topic is for reporting bugs and issues with GATK.
We'll get back to you if we have any updates or follow up questions. Please see our Support Policy for more details about how we prioritize responding to questions.
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Hi Michelle Lian,
Both of these "extra args" arguments are used to add flexibility to the WDL. They are kind of a catch all string so that if someone would like to run this pipeline but they want to alter some of Mutect's arguments they can use this WDL as is and just provide the arguments as inputs to the WDL (rather than having to edit the WDL to include more arguments).Both of the "extra args" arguments are optional, so you can run the pipeline without providing anything for them. If you are just trying to run Mutect on mitochondria yourself without using WDL, then you can also ignore these "extra args" arguments and remove them from your script.
I hope this helps!
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Hi Michelle,
We haven't heard from you in a while so we're going to close out this ticket in our system. If you still require assistance, simply respond to this thread and we'll be happy to pick up where we left off!
Kind regards,
Genevieve
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