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):.

• c76550b3e5bc1670539e4dbaa1202cbd NGHC_16_C_R1_sub.bait.interval_list
• c76550b3e5bc1670539e4dbaa1202cbd NGHC_16_C_R1_sub.target.interval_list

Yet the on target and on bait are different?

ON_BAIT_BASES 

• 1466323439

ON_TARGET_BASES

• 1199242329

Why is that?

Thanks!

Can you please provide

a) GATK version used

The Genome Analysis Toolkit (GATK) v4.1.7.0
HTSJDK Version: 2.21.2
Picard Version: 2.21.9

b) Exact GATK commands used

gatk CollectHsMetrics -BI /data/temp/T/NGHC_16_C_R1_sub.bait.interval_list -I /data/temp/T/NGHC_16_C_fixmate_novosort_dupsrmFalse.bam -O stats.tsv -TI /data/temp/T/NGHC_16_C_R1_sub.target.interval_list &> newest.log

c) The entire error log if applicable.

14:55:41.291 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data1/BIOINFORMATICS/SOFTWARE/ANACONDA_JN/MINI-CONDA/envs/gatk-newest/share/gatk4-4.1.7.0-0/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Jun 08 14:55:41 EDT 2020] CollectHsMetrics --BAIT_INTERVALS /data/temp/T/NGHC_16_C_R1_sub.bait.interval_list --TARGET_INTERVALS /data/temp/T/NGHC_16_C_R1_sub.target.interval_list --INPUT /data/temp/T/NGHC_16_C_fixmate_novosort_dupsrmFalse.bam --OUTPUT stats.tsv --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
Jun 08, 2020 2:55:41 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
[Mon Jun 08 14:55:41 EDT 2020] Executing as xxxx@xxxxx.com on Linux 3.10.0-1062.1.2.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_152-release-1056-b12; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.7.0
INFO 2020-06-08 14:55:57 CollectHsMetrics Processed 1,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 11s. Last read position: chr1:86,126,044
INFO 2020-06-08 14:56:08 CollectHsMetrics Processed 2,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 10s. Last read position: chr1:201,899,936
INFO 2020-06-08 14:56:20 CollectHsMetrics Processed 3,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 12s. Last read position: chr2:64,551,810
INFO 2020-06-08 14:56:31 CollectHsMetrics Processed 4,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 11s. Last read position: chr2:195,864,616
INFO 2020-06-08 14:56:43 CollectHsMetrics Processed 5,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 12s. Last read position: chr3:48,594,462
INFO 2020-06-08 14:56:55 CollectHsMetrics Processed 6,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 12s. Last read position: chr3:184,236,032
INFO 2020-06-08 14:57:06 CollectHsMetrics Processed 7,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 11s. Last read position: chr4:110,520,274
INFO 2020-06-08 14:57:18 CollectHsMetrics Processed 8,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 11s. Last read position: chr5:88,823,892
INFO 2020-06-08 14:57:29 CollectHsMetrics Processed 9,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 11s. Last read position: chr6:25,966,715
INFO 2020-06-08 14:57:41 CollectHsMetrics Processed 10,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 11s. Last read position: chr6:132,683,239
INFO 2020-06-08 14:57:52 CollectHsMetrics Processed 11,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 11s. Last read position: chr7:98,243,421
INFO 2020-06-08 14:58:04 CollectHsMetrics Processed 12,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 11s. Last read position: chr8:27,012,116
INFO 2020-06-08 14:58:15 CollectHsMetrics Processed 13,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 10s. Last read position: chr9:33,676,744
INFO 2020-06-08 14:58:25 CollectHsMetrics Processed 14,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 10s. Last read position: chr9:136,835,727
INFO 2020-06-08 14:58:36 CollectHsMetrics Processed 15,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 11s. Last read position: chr10:104,193,953
INFO 2020-06-08 14:58:47 CollectHsMetrics Processed 16,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 11s. Last read position: chr11:61,281,926
INFO 2020-06-08 14:58:58 CollectHsMetrics Processed 17,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 10s. Last read position: chr12:4,685,017
INFO 2020-06-08 14:59:08 CollectHsMetrics Processed 18,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 10s. Last read position: chr12:110,036,276
INFO 2020-06-08 14:59:18 CollectHsMetrics Processed 19,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 9s. Last read position: chr14:20,992,211
INFO 2020-06-08 14:59:28 CollectHsMetrics Processed 20,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 10s. Last read position: chr15:21,876,887
INFO 2020-06-08 14:59:37 CollectHsMetrics Processed 21,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 9s. Last read position: chr15:88,857,072
INFO 2020-06-08 14:59:47 CollectHsMetrics Processed 22,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 9s. Last read position: chr16:66,935,483
INFO 2020-06-08 14:59:56 CollectHsMetrics Processed 23,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 9s. Last read position: chr17:30,844,873
INFO 2020-06-08 15:00:06 CollectHsMetrics Processed 24,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 9s. Last read position: chr17:81,953,085
INFO 2020-06-08 15:00:15 CollectHsMetrics Processed 25,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 9s. Last read position: chr19:11,402,001
INFO 2020-06-08 15:00:25 CollectHsMetrics Processed 26,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 9s. Last read position: chr19:52,881,937
INFO 2020-06-08 15:00:35 CollectHsMetrics Processed 27,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 9s. Last read position: chr20:64,264,461
INFO 2020-06-08 15:00:44 CollectHsMetrics Processed 28,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 8s. Last read position: chr22:46,666,616
INFO 2020-06-08 15:00:53 CollectHsMetrics Processed 29,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 9s. Last read position: chrM:11,846
INFO 2020-06-08 15:00:54 TheoreticalSensitivity Creating Roulette Wheel
INFO 2020-06-08 15:00:54 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2020-06-08 15:00:54 TheoreticalSensitivity 0 sampling iterations completed
INFO 2020-06-08 15:00:55 TheoreticalSensitivity 1000 sampling iterations completed
INFO 2020-06-08 15:00:56 TheoreticalSensitivity 2000 sampling iterations completed
INFO 2020-06-08 15:00:57 TheoreticalSensitivity 3000 sampling iterations completed
INFO 2020-06-08 15:00:58 TheoreticalSensitivity 4000 sampling iterations completed
INFO 2020-06-08 15:00:59 TheoreticalSensitivity 5000 sampling iterations completed
INFO 2020-06-08 15:01:00 TheoreticalSensitivity 6000 sampling iterations completed
INFO 2020-06-08 15:01:01 TheoreticalSensitivity 7000 sampling iterations completed
INFO 2020-06-08 15:01:02 TheoreticalSensitivity 8000 sampling iterations completed
INFO 2020-06-08 15:01:03 TheoreticalSensitivity 9000 sampling iterations completed
INFO 2020-06-08 15:01:04 TheoreticalSensitivity Calculating theoretical het sensitivity
[Mon Jun 08 15:01:05 EDT 2020] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 5.40 minutes.