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freeseek / gtc2vcf

Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF
MIT License
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Final BCF not being created. #55

Closed mahaaamir closed 1 year ago

mahaaamir commented 1 year ago

Hello I am having an issue with the bcf, even though the BPM and all GTC files are being read in, at the final step the output says that it has 'skipped' all lines and is now merging 0 temporary files. This is the output I get (with the gtcs being read in collapsed): Writing to ./bcftools-sort.XXXXXXAR1U7c gtc2vcf 2022-01-12 https://github.com/freeseek/gtc2vcf Reading BPM file /home/GDA-8v1-0_D2.bpm Reading EGT file /home/GDA-8v1-0_D1_ClusterFile.egt Reading GTC file /2_R02C01.gtc Reading GTC file /5_R03C01.gtc Writing VCF file Lines total/missing-reference/skipped: 1904599/0/1904599 Merging 0 temporary files Cleaning Done This is the code that I am using: #!/bin/bash bpm_manifest_file="/home/GDA-8v1-0_D2.bpm" egt_cluster_file="/home/GDA-8v1-0_D1_ClusterFile.egt" path_to_gtc_folder="/HMC/GTCs" ref="/home/maamir/GR38.gz" out_prefix="HMCmine" bcftools +gtc2vcf \ --no-version -Ou \ --bpm $bpm_manifest_file \ --egt $egt_cluster_file \ --gtcs $path_to_gtc_folder \ --fasta-ref $ref \ --extra $out_prefix.tsv | \ bcftools sort -Ou -T ./bcftools-sort.XXXXXX | \ bcftools norm --no-version -Ob -c x -f $ref | \ tee $out_prefix.bcf | \ bcftools index --force --output $out_prefix.bcf.csi Could there be an issue with the indexing of my reference genome?

freeseek commented 1 year ago

The line:

total/missing-reference/skipped: 1904599/0/1904599

indicates that all variants were skipped. I am guessing that maybe the contig names in the reference might be an issue. Can you show the output of:

cat /home/maamir/GR38.gz.fai

You can also use the option -v to get a verbose stderr output but most likely it would just tell you that all variants are unlocalized

mahaaamir commented 1 year ago

Yes I believe there might be an issue with the reference. Here is the output I get- NC_000001.11 248956422 69 80 81 NT_187361.1 175055 252068568 80 81 NT_187362.1 32032 252245933 80 81 NT_187363.1 127682 252278487 80 81 NT_187364.1 66860 252407887 80 81 NT_187365.1 40176 252475704 80 81 NT_187366.1 42210 252516504 80 81 NT_187367.1 176043 252559363 80 81 NT_187368.1 40745 252737728 80 81 NT_187369.1 41717 252779104 80 81 NC_000002.12 242193529 252821412 80 81 NT_187370.1 161471 498042477 80 81 NT_187371.1 153799 498206083 80 81 NC_000003.12 198295559 498361874 80 81 NT_167215.1 155397 699136239 80 81 NC_000004.12 190214555 699293648 80 81 NT_113793.3 209709 891886001 80 81 NC_000005.10 181538259 892098401 80 81 NT_113948.1 92689 1075906005 80 81 NC_000006.12 170805979 1075999922 80 81 NC_000007.14 159345973 1248941045 80 81 NC_000008.11 145138636 1410278912 80 81 NC_000009.12 138394717 1557231850 80 81 NT_187372.1 40062 1697356622 80 81 NT_187373.1 38054 1697397306 80 81 NT_187374.1 176845 1697435957 80 81 NT_187375.1 39050 1697615134 80 81 NC_000010.11 133797422 1697654743 80 81 NC_000011.10 135086622 1833124703 80 81 NC_000012.12 133275309 1969899978 80 81 NC_000013.11 114364328 2104841299 80 81 NC_000014.9 107043718 2220635251 80 81 NT_113796.3 201709 2329017139 80 81 NT_167219.1 211173 2329221493 80 81 NT_187377.1 194050 2329435429 80 81 NT_113888.1 191469 2329632028 80 81 NT_187378.1 38115 2329826014 80 81 NT_187379.1 39555 2329864729 80 81 NT_187380.1 172810 2329904902 80 81 NT_187381.1 43739 2330079996 80 81 NC_000015.10 101991189 2330124352 80 81 NT_187382.1 448248 2433390549 80 81 NC_000016.10 90338345 2433844471 80 81 NT_187383.1 1872759 2525312164 80 81 NC_000017.11 83257441 2527208403 80 81 NT_113930.2 185591 2611506681 80 81 NT_187384.1 280839 2611694710 80 81 NT_187385.1 112551 2611979178 80 81 NC_000018.10 80373285 2612093206 80 81 NC_000019.10 58617616 2693471228 80 81 NC_000020.11 64444167 2752821635 80 81 NC_000021.9 46709983 2818071424 80 81 NC_000022.11 50818468 2865365352 80 81 NT_187386.1 150754 2916819174 80 81 NT_187387.1 41543 2916971936 80 81 NT_187388.1 179772 2917014122 80 81 NT_187390.1 42811 2917196265 80 81 NT_187391.1 181920 2917239735 80 81 NT_187392.1 103838 2917424052 80 81 NT_187393.1 99375 2917529311 80 81 NT_187394.1 73985 2917630052 80 81 NC_000023.11 156040895 2917705031 80 81 NC_000024.10 57227415 3075696507 80 81 NT_187395.1 37240 3133639381 80 81 NT_187396.1 2274 3133677187 80 81 NT_187397.1 2165 3133679590 80 81 NT_187398.1 1942 3133681883 80 81 NT_187399.1 1472 3133683950 80 81 NT_187400.1 21476 3133685541 80 81 NT_187401.1 4416 3133707386 80 81 NT_187402.1 1201 3133711958 80 81 NT_187403.1 1444 3133713275 80 81 NT_187404.1 2276 3133714838 80 81 NT_187405.1 998 3133717243 80 81 NT_187406.1 12399 3133718354 80 81 NT_187407.1 37690 3133731008 80 81 NT_187408.1 1179 3133769270 80 81 NT_187409.1 2646 3133770564 80 81 NT_187410.1 2489 3133773344 80 81 NT_187411.1 1029 3133775965 80 81 NT_187412.1 2145 3133777107 80 81 NT_187413.1 2321 3133779379 80 81 NT_187414.1 2140 3133781830 80 81 NT_187415.1 2043 3133784097 80 81 NT_187416.1 1445 3133786266 80 81 NT_187417.1 981 3133787830 80 81 NT_187418.1 1884 3133788924 80 81 NT_187419.1 1361 3133790932 80 81 NT_187420.1 392061 3133792411 80 81 NT_187421.1 1233 3134189473 80 81 NT_187422.1 1774 3134190822 80 81 NT_187423.1 3920 3134192719 80 81 NT_187424.1 92983 3134196788 80 81 NT_187425.1 112505 3134291034 80 81 NT_187426.1 4055 3134405046 80 81 NT_187427.1 2415 3134409252 80 81 NT_187428.1 2318 3134411798 80 81 NT_187429.1 2186 3134414245 80 81 NT_187430.1 1951 3134416559 80 81 NT_187431.1 1300 3134418635 80 81 NT_187432.1 22689 3134420052 80 81 NT_187433.1 138126 3134443125 80 81 NT_187434.1 5674 3134583078 80 81 NT_187435.1 8127 3134588923 80 81 NT_187436.1 6361 3134597252 80 81 NT_187437.1 5353 3134603793 80 81 NT_187438.1 3253 3134609313 80 81 NT_187439.1 1899 3134612707 80 81 NT_187440.1 2983 3134614730 80 81 NT_187441.1 2168 3134617851 80 81 NT_187442.1 993 3134620147 80 81 NT_187443.1 91309 3134621253 80 81 NT_187444.1 1202 3134713804 80 81 NT_187445.1 1599 3134715122 80 81 NT_187446.1 1400 3134716841 80 81 NT_187447.1 2969 3134718359 80 81 NT_187448.1 1553 3134721466 80 81 NT_187449.1 7046 3134723139 80 81 NT_187450.1 31033 3134730374 80 81 NT_187451.1 44474 3134761895 80 81 NT_187452.1 4685 3134807025 80 81 NT_187453.1 4513 3134811869 80 81 NT_187454.1 6504 3134816539 80 81 NT_187455.1 6158 3134823225 80 81 NT_187456.1 3041 3134829560 80 81 NT_187457.1 5796 3134832740 80 81 NT_187458.1 1652 3134838709 80 81 NT_187459.1 1040 3134840482 80 81 NT_187460.1 1368 3134841635 80 81 NT_187461.1 2699 3134843121 80 81 NT_187462.1 1048 3134845954 80 81 NT_187463.1 1428 3134847116 80 81 NT_187464.1 1428 3134848662 80 81 NT_187465.1 1026 3134850208 80 81 NT_187466.1 1121 3134851347 80 81 NT_187467.1 1803 3134852583 80 81 NT_187468.1 2855 3134854509 80 81 NT_187469.1 3530 3134857500 80 81 NT_187470.1 8320 3134861175 80 81 NT_187471.1 1048 3134869699 80 81 NT_187472.1 1045 3134870861 80 81 NT_187473.1 1298 3134872020 80 81 NT_187474.1 2387 3134873435 80 81 NT_187475.1 1537 3134875952 80 81 NT_187476.1 1143 3134877609 80 81 NT_187477.1 1880 3134878867 80 81 NT_187478.1 1216 3134880871 80 81 NT_187479.1 970 3134882203 80 81 NT_187480.1 1788 3134883286 80 81 NT_187481.1 1484 3134885197 80 81 NT_187482.1 1750 3134886800 80 81 NT_187483.1 1308 3134888672 80 81 NT_187484.1 1658 3134890097 80 81 NT_187485.1 971 3134891876 80 81 NT_187486.1 1930 3134892960 80 81 NT_187487.1 990 3134895015 80 81 NT_187488.1 4215 3134896118 80 81 NT_187489.1 1136 3134900486 80 81 NT_187490.1 2656 3134901737 80 81 NT_187491.1 1650 3134904527 80 81 NT_187492.1 1451 3134906298 80 81 NT_187493.1 2378 3134907868 80 81 NT_187494.1 2805 3134910376 80 81 NT_187495.1 7992 3134913317 80 81 NT_187496.1 7642 3134921509 80 81 NT_113901.1 182896 3134929348 80 81 NT_167213.1 179198 3135114633 80 81 NT_167214.1 161802 3135296173 80 81 NT_167218.1 179693 3135460100 80 81 NT_187497.1 157432 3135642142 80 81 NT_167220.1 15008 3135801644 80 81 NT_167208.1 164239 3135816941 80 81 NT_187498.1 210658 3135983335 80 81 NT_187499.1 168472 3136196729 80 81 NT_187500.1 41891 3136367409 80 81 NT_187501.1 66486 3136409926 80 81 NT_187502.1 198735 3136477346 80 81 NT_187503.1 93321 3136678668 80 81 NT_187504.1 158759 3136773258 80 81 NT_187505.1 148850 3136934104 80 81 NT_187506.1 150742 3137084917 80 81 NT_187508.1 62944 3137237646 80 81 NT_187509.1 40191 3137301479 80 81 NT_187510.1 36723 3137342275 80 81 NT_187511.1 79590 3137379560 80 81 NT_187512.1 71251 3137460247 80 81 NT_167209.1 137718 3137532490 80 81 NT_187513.1 186739 3137672032 80 81 NT_167211.2 176608 3137861207 80 81 NT_113889.1 161147 3138040124 80 81 NW_012132914.1 467143 3138203394 80 81 NW_015495298.1 278659 3138676481 80 81 NW_025791756.1 1572686 3138958737 80 81 NW_011332688.1 305542 3140551183 80 81 NW_014040926.1 349938 3140860649 80 81 NW_009646195.1 166200 3141215063 80 81 NW_018654706.1 166136 3141383445 80 81 NW_019805487.1 44955 3141551758 80 81 NW_009646194.1 186494 3141597375 80 81 NW_018654707.1 140355 3141786305 80 81 NW_014040925.1 141019 3141928519 80 81 NW_017852928.1 551020 3142071405 80 81 NW_009646196.1 122022 3142629414 80 81 NW_025791753.1 516764 3142753067 80 81 NW_025791758.1 211934 3143276392 80 81 NW_025791759.1 250447 3143491077 80 81 NW_025791754.1 847441 3143744760 80 81 NW_011332687.1 460100 3144602896 80 81 NW_018654708.1 330031 3145068849 80 81 NW_014040927.1 212205 3145403113 80 81 NW_025791757.1 210426 3145618072 80 81 NW_025791755.1 335159 3145831234 80 81 NW_021159988.1 84043 3146170684 80 81 NW_025791767.1 244725 3146255886 80 81 NW_025791768.1 174385 3146503772 80 81 NW_025791766.1 489404 3146680438 80 81 NW_025791763.1 284971 3147176064 80 81 NW_012132915.1 481245 3147464699 80 81 NW_025791760.1 431782 3147952067 80 81 NW_025791765.1 955087 3148389348 80 81 NW_018654709.1 181658 3149356480 80 81 NW_025791762.1 500581 3149540516 80 81 NW_025791761.1 535251 3150047462 80 81 NW_025791764.1 120381 3150589505 80 81 NW_015495299.1 535088 3150711497 80 81 NW_018654710.1 140361 3151253380 80 81 NW_011332690.1 365499 3151395597 80 81 NW_021159987.1 145975 3151765765 80 81 NW_011332689.1 208149 3151913666 80 81 NW_017363813.1 411654 3152124518 80 81 NW_025791770.1 301310 3152541419 80 81 NW_025791771.1 475876 3152846597 80 81 NW_009646197.1 451168 3153328523 80 81 NW_012132916.1 373699 3153785432 80 81 NW_011332691.1 415308 3154163903 80 81 NW_021159989.1 215443 3154584507 80 81 NW_018654711.1 175849 3154802748 80 81 NW_012132917.1 165718 3154980897 80 81 NW_009646198.1 305979 3155148788 80 81 NW_019805491.1 105527 3155458693 80 81 NW_019805492.1 195063 3155565646 80 81 NW_019805490.1 302885 3155763254 80 81 NW_019805489.1 197752 3156070032 80 81 NW_019805488.1 164041 3156270362 80 81 NW_025791769.1 469342 3156436555 80 81 NW_021159990.1 235734 3156911864 80 81 NW_021159993.1 176674 3157150646 80 81 NW_013171799.1 90922 3157329633 80 81 NW_025791774.1 205691 3157421792 80 81 NW_021159992.1 53476 3157630156 80 81 NW_021159994.1 125549 3157684402 80 81 NW_021159991.1 341066 3157811622 80 81 NW_021159995.1 276109 3158157052 80 81 NW_013171800.1 163749 3158436718 80 81 NW_013171801.1 236512 3158602619 80 81 NW_025791772.1 308682 3158842194 80 81 NW_017363814.1 420675 3159154841 80 81 NW_025791773.1 113364 3159580876 80 81 NW_015495301.1 205407 3159695764 80 81 NW_015495300.1 230434 3159903840 80 81 NW_025791777.1 2101585 3160137256 80 81 NW_018654712.1 135987 3162265215 80 81 NW_025791776.1 208405 3162403003 80 81 NW_009646199.1 139087 3162614118 80 81 NW_016107297.1 362221 3162755048 80 81 NW_025791779.1 302485 3163121902 80 81 NW_021159996.1 89956 3163428270 80 81 NW_025791778.1 508332 3163519452 80 81 NW_016107298.1 673059 3164034238 80 81 NW_025791775.1 34400 3164715812 80 81 NW_018654713.1 242796 3164750743 80 81 NW_013171803.1 82315 3164996679 80 81 NW_025791780.1 383128 3165080127 80 81 NW_012132918.1 320750 3165468146 80 81 NW_009646200.1 268330 3165793007 80 81 NW_013171802.1 245716 3166064793 80 81 NW_017363815.1 139427 3166313682 80 81 NW_021159997.1 73265 3166454952 80 81 NW_021159998.1 254759 3166529234 80 81 NW_019805493.1 172555 3166787282 80 81 NW_025791781.1 464417 3166962098 80 81 NW_017852929.1 142129 3167432422 80 81 NW_017852930.1 468267 3167576429 80 81 NW_018654714.1 589656 3168050650 80 81 NW_018654715.1 680662 3168647783 80 81 NW_012132919.1 179932 3169337055 80 81 NW_025791785.1 429744 3169519338 80 81 NW_018654717.1 6367528 3169954553 80 81 NW_017852932.1 265876 3176401777 80 81 NW_025791782.1 150302 3176671078 80 81 NW_017852931.1 156998 3176823360 80 81 NW_025791784.1 106905 3176982422 80 81 NW_019805494.1 103072 3177090768 80 81 NW_025791786.1 207371 3177195230 80 81 NW_018654716.1 165120 3177405295 80 81 NW_025791783.1 39290 3177572580 80 81 NW_013171804.1 163882 3177612466 80 81 NW_013171805.1 134099 3177778501 80 81 NW_025791789.1 569668 3177914378 80 81 NW_025791787.1 340717 3178491268 80 81 NW_025791788.1 482250 3178836345 80 81 NW_009646201.1 330164 3179324725 80 81 NW_021159999.1 25408 3179659117 80 81 NW_021160000.1 454963 3179684944 80 81 NW_011332694.1 420164 3180145704 80 81 NW_021160001.1 292944 3180571223 80 81 NW_013171806.1 185507 3180867935 80 81 NW_009646202.1 277797 3181055863 80 81 NW_013171807.1 264545 3181337235 80 81 NW_025791790.1 196262 3181605189 80 81 NW_011332693.1 85284 3181804014 80 81 NW_011332692.1 14347 3181890467 80 81 NW_015148966.2 204999 3181905102 80 81 NW_025791792.1 434831 3182112765 80 81 NW_021160004.1 270122 3182553132 80 81 NW_025791794.1 122722 3182826733 80 81 NW_011332695.1 203552 3182951098 80 81 NW_021160006.1 170928 3183157297 80 81 NW_019805496.1 279644 3183330464 80 81 NW_019805495.1 305244 3183613706 80 81 NW_017363816.1 140877 3183922868 80 81 NW_025791793.1 344606 3184065608 80 81 NW_019805498.1 181167 3184414630 80 81 NW_021160005.1 217075 3184598164 80 81 NW_021160003.1 165419 3184818055 80 81 NW_019805497.1 301637 3184985648 80 81 NW_013171808.1 181958 3185291158 80 81 NW_021160002.1 45257 3185475493 80 81 NW_025791791.1 261194 3185521424 80 81 NW_009646203.1 108875 3185785985 80 81 NW_013171809.1 109323 3185896327 80 81 NW_018654718.1 1046838 3186007119 80 81 NW_021160008.1 192531 3187067145 80 81 NW_011332696.1 541038 3187262185 80 81 NW_009646204.1 211377 3187810086 80 81 NW_025791795.1 104537 3188024208 80 81 NW_018654720.1 174808 3188130160 80 81 NW_015148967.1 315610 3188307256 80 81 NW_018654719.1 64689 3188626914 80 81 NW_011332697.1 86533 3188692514 80 81 NW_019805499.1 154139 3188780237 80 81 NW_021160007.1 297568 3188936419 80 81 NW_021160012.1 409912 3189237809 80 81 NW_011332699.1 356766 3189652947 80 81 NW_013171810.1 168146 3190014279 80 81 NW_021160009.1 7309 3190184631 80 81 NW_009646205.1 35455 3190192134 80 81 NW_011332700.1 148762 3190228135 80 81 NW_013171811.1 123480 3190378863 80 81 NW_021160010.1 158944 3190503989 80 81 NW_021160011.1 65394 3190665022 80 81 NW_011332698.1 206320 3190731343 80 81 NW_021160013.1 399183 3190940344 80 81 NW_025791796.1 722645 3191344626 80 81 NW_018654722.1 690932 3192076404 80 81 NW_021160014.1 264228 3192776079 80 81 NW_018654721.1 171798 3193043716 80 81 NW_011332701.1 4998962 3193217764 80 81 NW_021160018.1 396515 3198279316 80 81 NW_021160017.1 5500449 3198680890 80 81 NW_012132920.1 2365364 3204250201 80 81 NW_025791798.1 204007 3206645239 80 81 NW_021160016.1 369264 3206851899 80 81 NW_025791797.1 1154574 3207225881 80 81 NW_021160015.1 97763 3208394990 80 81 NW_025791799.1 87715 3208494077 80 81 NW_013171812.1 59016 3208582995 80 81 NW_019805500.1 480415 3208642851 80 81 NW_017852933.1 1927115 3209129373 80 81 NW_021160019.1 270967 3211080679 80 81 NW_013171813.1 267463 3211355142 80 81 NW_018654723.1 78609 3211626057 80 81 NW_012132921.1 169136 3211705757 80 81 NW_025791800.1 334997 3211877109 80 81 NW_017363817.1 281919 3212216409 80 81 NW_021160020.1 137908 3212501954 80 81 NW_016107299.1 154723 3212641688 80 81 NW_017363819.1 276292 3212798452 80 81 NW_025791803.1 538541 3213078300 80 81 NW_025791801.1 372839 3213623680 80 81 NW_017363818.1 246895 3214001287 80 81 NW_019805501.1 116753 3214251376 80 81 NW_025791806.1 172609 3214369691 80 81 NW_025791802.1 234878 3214544560 80 81 NW_025791805.1 187626 3214782476 80 81 NW_021160021.1 56695 3214972550 80 81 NW_025791804.1 144689 3215030056 80 81 NW_019805503.1 163186 3215176660 80 81 NW_014040928.1 205101 3215341994 80 81 NW_019805502.1 230843 3215549761 80 81 NW_013171814.1 407387 3215783592 80 81 NW_018654724.1 93070 3216196174 80 81 NW_025791809.1 226166 3216290510 80 81 NW_025791810.1 89211 3216519610 80 81 NW_025791807.1 333754 3216610039 80 81 NW_021160022.1 493165 3216948066 80 81 NW_014040929.1 405389 3217447496 80 81 NW_025791808.1 137818 3217858055 80 81 NW_009646206.1 370917 3217997698 80 81 NW_016107300.1 163926 3218373373 80 81 NW_016107301.1 170206 3218539470 80 81 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freeseek commented 1 year ago

Yes, you need contig names that can be matched to the contig names in the .bpm manifest file. There is a dictionary in the file hg38.chromAlias.txt but I don't know of a standard tool that will perform the conversion for you. Unrelated but also notice that without the option -c/--csv indel variants will not be converted to VCF correctly. You need all .bpm, .egt, and .csv manifest files for a proper conversion

mahaaamir commented 1 year ago

Is the csv file just the manifest in csv format?

freeseek commented 1 year ago

Almost. The .csv usually contains more information than the .bpm, like flank and probe sequences which are needed for converting indels. However, the .csv does not contain the order of the normalization bins (this is what you get with the --beadset-order option) so for proper conversion of a GTC file you really need both