
JonR
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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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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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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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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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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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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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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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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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That worked. Thank you Tiffany Miller!