I am using a multisample vcf file to test if any sample is contaminated.
Here is the command and log.
$ ./sceVCF -o cont_check.tvs /mnt/e/DATA_ANALYSIS/SA_samples/rawSA.g5mac3dplm.sorted_rename.vcf.gz
[12:08:20-385] - INFO: SCE-VCF v0.1.3
[12:08:20-385] - ARG: Input VCF: @["/mnt/e/DATA_ANALYSIS/SA_samples/rawSA.g5mac3dplm.sorted_rename.vcf.gz"]
[12:08:20-385] - ARG: Output: cont_check.tvs
[12:08:20-385] - ARG: AD field: AD
[12:08:20-385] - ARG: AF field: AF
[12:08:20-385] - ARG: Is refAF: false
[12:08:20-385] - ARG: REF AF limits: 0.1,0.9
[12:08:20-385] - ARG: Het AB limit: 0.25,0.75
[12:08:20-385] - ARG: Min GQ: 20
[12:08:20-385] - ARG: DP limit: 20,100
[12:08:20-389] - INFO: Variant processing started
[12:08:20-389] - INFO: Processing file /mnt/e/DATA_ANALYSIS/SA_samples/rawSA.g5mac3dplm.sorted_rename.vcf.gz
[12:08:24-787] - INFO: 50000 variants processed. Last batch: 50000 in 2 seconds and 143 milliseconds
[12:08:29-120] - INFO: 100000 variants processed. Last batch: 50000 in 2 seconds and 335 milliseconds
[12:08:33-702] - INFO: 150000 variants processed. Last batch: 50000 in 2 seconds and 413 milliseconds
[12:08:37-886] - INFO: 200000 variants processed. Last batch: 50000 in 2 seconds and 237 milliseconds
[12:08:42-178] - INFO: 250000 variants processed. Last batch: 50000 in 2 seconds and 324 milliseconds
[12:08:46-595] - INFO: 300000 variants processed. Last batch: 50000 in 2 seconds and 430 milliseconds
[12:08:50-993] - INFO: 350000 variants processed. Last batch: 50000 in 2 seconds and 386 milliseconds
[12:08:55-555] - INFO: 400000 variants processed. Last batch: 50000 in 2 seconds and 391 milliseconds
[12:08:59-782] - INFO: 450000 variants processed. Last batch: 50000 in 2 seconds and 121 milliseconds
[12:09:03-903] - INFO: 500000 variants processed. Last batch: 50000 in 2 seconds and 194 milliseconds
[12:09:11-882] - INFO: 600000 variants processed. Last batch: 100000 in 4 seconds and 287 milliseconds
[12:09:19-982] - INFO: 700000 variants processed. Last batch: 100000 in 4 seconds and 359 milliseconds
[12:09:27-972] - INFO: 800000 variants processed. Last batch: 100000 in 4 seconds and 380 milliseconds
[12:09:36-317] - INFO: 900000 variants processed. Last batch: 100000 in 4 seconds and 526 milliseconds
[12:09:44-318] - INFO: 1000000 variants processed. Last batch: 100000 in 4 seconds and 329 milliseconds
[12:10:10-829] - INFO: 1339101 variants processed, 1339101 vars ignored
[12:10:10-829] - INFO: 0 no PASS variants, 1339101 not in autosomes, 0 multiallelic, 0 indels, 0 outside ref AF limits, 0 missing AF tag
[12:10:10-829] - FATAL: No variants remaining for analysis
I am using a multisample vcf file to test if any sample is contaminated.
Here is the command and log.
$ ./sceVCF -o cont_check.tvs /mnt/e/DATA_ANALYSIS/SA_samples/rawSA.g5mac3dplm.sorted_rename.vcf.gz
[12:08:20-385] - INFO: SCE-VCF v0.1.3
[12:08:20-385] - ARG: Input VCF: @["/mnt/e/DATA_ANALYSIS/SA_samples/rawSA.g5mac3dplm.sorted_rename.vcf.gz"]
[12:08:20-385] - ARG: Output: cont_check.tvs
[12:08:20-385] - ARG: AD field: AD
[12:08:20-385] - ARG: AF field: AF
[12:08:20-385] - ARG: Is refAF: false
[12:08:20-385] - ARG: REF AF limits: 0.1,0.9
[12:08:20-385] - ARG: Het AB limit: 0.25,0.75
[12:08:20-385] - ARG: Min GQ: 20
[12:08:20-385] - ARG: DP limit: 20,100
[12:08:20-389] - INFO: Variant processing started
[12:08:20-389] - INFO: Processing file /mnt/e/DATA_ANALYSIS/SA_samples/rawSA.g5mac3dplm.sorted_rename.vcf.gz
[12:08:24-787] - INFO: 50000 variants processed. Last batch: 50000 in 2 seconds and 143 milliseconds
[12:08:29-120] - INFO: 100000 variants processed. Last batch: 50000 in 2 seconds and 335 milliseconds
[12:08:33-702] - INFO: 150000 variants processed. Last batch: 50000 in 2 seconds and 413 milliseconds
[12:08:37-886] - INFO: 200000 variants processed. Last batch: 50000 in 2 seconds and 237 milliseconds
[12:08:42-178] - INFO: 250000 variants processed. Last batch: 50000 in 2 seconds and 324 milliseconds
[12:08:46-595] - INFO: 300000 variants processed. Last batch: 50000 in 2 seconds and 430 milliseconds
[12:08:50-993] - INFO: 350000 variants processed. Last batch: 50000 in 2 seconds and 386 milliseconds
[12:08:55-555] - INFO: 400000 variants processed. Last batch: 50000 in 2 seconds and 391 milliseconds
[12:08:59-782] - INFO: 450000 variants processed. Last batch: 50000 in 2 seconds and 121 milliseconds
[12:09:03-903] - INFO: 500000 variants processed. Last batch: 50000 in 2 seconds and 194 milliseconds
[12:09:11-882] - INFO: 600000 variants processed. Last batch: 100000 in 4 seconds and 287 milliseconds
[12:09:19-982] - INFO: 700000 variants processed. Last batch: 100000 in 4 seconds and 359 milliseconds
[12:09:27-972] - INFO: 800000 variants processed. Last batch: 100000 in 4 seconds and 380 milliseconds
[12:09:36-317] - INFO: 900000 variants processed. Last batch: 100000 in 4 seconds and 526 milliseconds
[12:09:44-318] - INFO: 1000000 variants processed. Last batch: 100000 in 4 seconds and 329 milliseconds
[12:10:10-829] - INFO: 1339101 variants processed, 1339101 vars ignored
[12:10:10-829] - INFO: 0 no PASS variants, 1339101 not in autosomes, 0 multiallelic, 0 indels, 0 outside ref AF limits, 0 missing AF tag
[12:10:10-829] - FATAL: No variants remaining for analysis