Test data on the hg38 human reference genome

Katerina Oleynikova

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Apr 7, 2021, 4:04:58 AM4/7/21

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Good day!

I would like to get any sample data for tests (on hg38/grch38) if it is possible. Thanks!

Uday Evani

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Apr 9, 2021, 3:52:56 PM4/9/21

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If you are just looking for sample data on GRCh38 you could consider using the high coverage 1000 Genomes data. Here is a CRAM file for sample NA12878, ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239334/NA12878.final.cram

MELT calls on this sample as part of the 1000 Genomes cohort is available here, http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage_SV/working/20190906_Devine_MELT/

Katerina Oleynikova

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Apr 14, 2021, 4:14:48 AM4/14/21

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Ok, thanks a lot!

пятница, 9 апреля 2021 г. в 22:52:56 UTC+3, uday...@gmail.com:

Katerina Oleynikova

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Apr 14, 2021, 4:39:50 AM4/14/21

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Btw, does MELT run on the small-sized data? In my opinion, ~12Gb is so huge for tests.. anyway, thanks a lot for your help!

пятница, 9 апреля 2021 г. в 22:52:56 UTC+3, uday...@gmail.com:

If you are just looking for sample data on GRCh38 you could consider using the high coverage 1000 Genomes data. Here is a CRAM file for sample NA12878, ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239334/NA12878.final.cram

egar...@umaryland.edu

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Apr 14, 2021, 4:51:55 AM4/14/21

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Hello,

MELT does work on the low coverage NA12878 sample, but this is about the smallest file that MELT will run well on. It does not work with sliced bams.