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Big variance of PCT_BASES_20X between software versions
I'm seeing a big variance of PCT_TARGET_BASES_20X between software versions and bed files Same bed files and interval files. Just change the software versions and mark duplicates True & False PCT_...
Same bed files, Different results (On Target vs On Bait)
My interval files are exactly the same, yet I get different on target and on bait metrics. Why? Thanks! More info: My interval files are exactly the same (confirmed via md5sum):. c76550b3e5...
GATK184.108.40.206 specific error: "htsjdk.samtools.SAMException: Cannot read non-existent file:"
Files work with multiple versions of GATK. From 220.127.116.11 to the older picard. However, I can't get the same command to work with 18.104.22.168. With newest program I was getting: htsjdk.samtools.SAMEx...
HS_PENALTY_20X is -1 on one version of GATK, crashes on newest version.
When running GATK 22.214.171.124 this works fine but I get a HS_PENALTY_20X of -1 It errors out on GATK v126.96.36.199 I assume a -1 for HS_PENALTY_20X is incorrect? # CONFIRMING FILES EXIST # ===============...
MINIMUM_PCT for picard.jar CollectInsertSizeMetrics
Other than trial & error, how do you know what to set MINIMUM_PCT at for picard.jar CollectInsertSizeMetrics? With this data-set it crashes at 0.15 but works for 0.16. I had to run the job about...