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Mandatory `--intervals` in GetPileupSummaries 220.127.116.11
Hello - I noticed that in
GetPileupSummaries from gatk 18.104.22.168 the argument
--intervals has become mandatory. (It was optional in, at least, 22.214.171.124). 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!
gatk GetPileupSummaries Using GATK jar /home/db291g/applications/gatk/gatk-126.96.36.199/gatk-package-188.8.131.52-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/db291g/applications/gatk/gatk-184.108.40.206/gatk-package-220.127.116.11-local.jar GetPileupSummaries **BETA FEATURE - WORK IN PROGRESS** USAGE: GetPileupSummaries [arguments] Tabulates pileup metrics for inferring contamination Version:18.104.22.168 Required Arguments: --input,-I:String BAM/SAM/CRAM file containing reads This argument must be specified at least once. Required. --intervals,-L:String One or more genomic intervals over which to operate This argument must be specified at least once. Required. --output,-O:File The output table Required. --variant,-V:FeatureInput A VCF file containing variants and allele frequencies Required.