JonR
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Latest activity by JonR-
JonR commented,
Ok file uploaded. GATKBUG-Brandt-JonR.tar.gz Check out the readme contained within. Simply activate the GATK conda environment, run the script and you should have all the files created from ...
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JonR commented,
My commands mkdir -p R3e_MAP_READS mkdir -p R3f_SAM_TO_BAM mkdir -p R3g_FIXMATE mkdir -p R3n_BED_TO_INTERVAL_LIST mkdir -p R3h_SORT mkdir -p R3q_REMOVE_DUPLICATES_FALSE mkdir -p R3j_REMOVE_DUPLICA...
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JonR commented,
Every part of this pipeline was done with the newest version of GATk4. I installed it today. I started from a sam file and every operation was ran today #GATK-4 FALSE FOLD_80_BASE_PENALTY 4.9...
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JonR commented,
CollectHsMetrics command FALSE # gatk CollectHsMetrics --TMP_DIR TEMP --BAIT_INTERVALS R3n_BED_TO_INTERVAL_LIST/XXXXHyper_1_C_50.7X_bait.interval_list --BAIT_SET_NAME DESIGN --TARGET_INTERVALS R3...
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JonR commented,
I just updated GATK-4 to the newest version 4.1.8 and ran it. These are the results got with CollectHsMetrics. Keep in mind bam files were still created with version 4.0.0.0-0. I can redo the e...
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JonR commented,
For PCT_TARGET_BASES_50X version 4.0.00.00 0.724252 gatk4-4.1.7.0-0 0.068928 This is with picard remove duplicates set to true. Doesn't seem to have an issue with false.
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JonR commented,
version 4.0.00.00 gatk-launch CollectHsMetrics --TMP_DIR TEMP --BAIT_INTERVALS R3n_BED_TO_INTERVAL_LIST/HG02026_HPR_Rep2_Cap04_70Me_30M_bait.interval_list --BAIT_SET_NAME DESIGN --TARGET_INTERVAL...
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JonR commented,
Hello Genenvieve, Then compare gatk4-4.0.0.0-0 vs the newest version. At 50x I'm getting 72% vs 6% coverage on one of my datasets. That's a 66% difference.
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JonR created a post,
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_...
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JonR created a post,
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...