Hello - I noticed that in GetPileupSummaries from gatk 4.0.8.1 the argument --intervals has become mandatory. (It was optional in, at least, 4.0.4.0). What is the reason for this change? I cannot see this change in the release notes, any chance this is a mishap during updates?
As always- thanks a lot for the feedback!
--input,-I:String             BAM/SAM/CRAM file containing reads  This argument must be specified at least once.
--output,-O:File              The output table  Required.
--variant,-V:FeatureInput     A VCF file containing variants and allele frequencies  Required.
Have you tried running the tool without --intervals? Does it not run? This may very well be a mistake, but I need to check with the team.
If true, adds a command line header line to created VCF files.  Default value: true.
specified 0 or more times. Default value: null.
cloudPrefetchBuffer if unset.  Default value: -1.
Size of the cloud-only prefetch buffer (in MB; 0 to disable).  Default value: 40.
If true, create a MD5 digest for any BAM/SAM/CRAM file created  Default value: false.
If specified, do not check the sequence dictionaries from our inputs for compatibility.
or more times. Default value: null.
--gatk-config-file:String     A configuration file to use with the GATK.  Default value: null.
Amount of padding (in bp) to add to each interval you are excluding.  Default value: 0.
--interval-padding,-ip:IntegerAmount of padding (in bp) to add to each interval you are including.  Default value: 0.
downsampled. Set to 0 to disable.  Default value: 0.
Maximum population allele frequency of sites to consider.  Default value: 0.2.
Minimum read mapping quality  Default value: 50.
at the expense of speed.  Default value: 0.01.
--reference,-R:String         Reference sequence  Default value: null.
Output traversal statistics every time this many seconds elapse  Default value: 10.0.
.dict file.  Default value: null.
If true, don't emit genotype fields when writing vcf file output.  Default value: false.
--TMP_DIR:File                Undocumented option  This argument may be specified 0 or more times. Default value: null.
Whether to use the JdkDeflater (as opposed to IntelDeflater)  Default value: false.
Whether to use the JdkInflater (as opposed to IntelInflater)  Default value: false.
Hi @dariober I ran into this as well. By passing the vcf file into the --intervals or -L, the tool completed. I raised a ticket so that the documentation in the tool gets updated. It says --intervals needs a string, but I passed a file.
I noticed this change as well, it says here that -L and -V can be identical?
I am sorry but i didn't quite catch the question you are asking.