How to generate RefSeq ROD

jderondejderonde Posts: 2Member

Dear team,

I would like to include a RefSeq ROD file in order to get the coverage per gene using the GATK coverage tool (http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html). However, it is not really clear to me how I can easily generate such a file, since I can not find the right documentation. All the links that should point to this information seem to be (incorrectly?) redirected to the main GATK homepage). For example this http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_utils_codecs_refseq_RefSeqCodec.html has a link that points to http://www.broadinstitute.org/gsa/wiki/index.php/RefSeq which is redirected to http://www.broadinstitute.org/gatk/. Can someone point me to the correct docs? Other resources I found also point to the same wiki, which I can't find at the moment..

Kind regards, JJ

Best Answer

Answers

  • mxqianmxqian Posts: 4Member

    Hi, When using the DepthOfCoverage, I got very strange ERROR MESSAGE as below. The program goes well to INFO 17:02:30,037 ProgressMeter - chrY:59358254 2.28041336E8 2.2 h 34.0 s 100.0% 2.2 h 0.0 s INFO 17:02:30,773 GATKRunReport - Uploaded run statistics report to AWS S3.

    And result for "per locus coverage" can be generated but other summary not. I count the numbers of exons and exon frameshifts and the number is exact 131. This transcript surely has too many exons.

    ##### ERROR MESSAGE: Unknown file is malformed: Data format error: numbers of exons and exon frameshifts differ for line=26 NM_001278267 chr1 + 144146810 146467744 144158383 146466121 131 144146810,144148789,144149726,144150981,144151518,144153012,144156971,144158177,144158378,144158870,144164518,144179473,144180355,144181063,144181950,144182695,144183587,144184251,144185133,144185827,144186714,144187459,144188351,144189011,144189893,144190581,144191468,144192205,144193097,144193759,144194641,144195343,144196230,144196975,144197867,144201704,144202586,144203298,144204185,144204924,144205816,144216027,144216909,144217611,144218498,144219235,144220127,144220786,144221668,144222378,144223265,144224002,144824704,145313333,145314215,145314903,145315790,145316511,145317405,145318053,145318935,145319623,145320510,145330682,145331574,145332222,145333104,145333796,145334683,145335388,145336280,145336928,145337810,145338516,145339403,145340108,145341000,145341648,145342530,145343240,145344127,145344832,145345724,145346372,145347254,145347964,145348851,145349562,145350454,145351102,145351984,145352684,145353571,145354294,145355186,145355836,145362978,145363678,145364565,146420018,146420910,146421558,146422440,146423162,146424049,146424783,146425675,146426323,146427205,146427927,146428814,146435853,146436735,146437457,146438344,146443692,146444574,146445298,146446923,146447725,146448373,146454019,146454737,146455624,146456358,146462010,146462657,146463539,146464263,146465150,146465877, 144147021,144148892,144149941,144151054,144151724,144153064,144157135,144158252,144158391,144159043,144164570,144179646,144180407,144181236,144182059,144182868,144183639,144184424,144185185,144186000,144186823,144187632,144188403,144189184,144189945,144190754,144191577,144192378,144193149,144193932,144194693,144195516,144196339,144197148,144197919,144201877,144202638,144203471,144204294,144205097,144205868,144216200,144216961,144217784,144218607,144219408,144220179,144220959,144221720,144222551,144223374,144224175,144824756,145313506,145314267,145315076,145315899,145316684,145317457,145318226,145318987,145319796,145320619,145330855,145331626,145332395,145333156,145333969,145334792,145335561,145336332,145337101,145337862,145338689,145339512,145340281,145341052,145341821,145342582,145343413,145344236,145345005,145345776,145346545,145347306,145348137,145348960,145349735,145350506,145351275,145352036,145352857,145353680,145354467,145355238,145356009,145363030,145363851,145364674,146420191,146420962,146421731,146422492,146423335,146424158,146424956,146425727,146426496,146427257,146428100,146428923,146436026,146436787,146437630,146438453,146443865,146444626,146445388,146447006,146447777,146448546,146454071,146454910,146455733,146456531,146462062,146462830,146463591,146464436,146465259,146467744, 0 NBPF20 cmpl cmpl -1,-1,-1,-1,-1,-1,-1,-1,0,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,2,1,2,1,2,1

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,660Administrator, GATK Developer admin

    @mxqian It sounds like your input file has a problem. Unfortunately we cannot help you with that. You will need to fix the difference or skip this locus.

    Geraldine Van der Auwera, PhD

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