Prepare table of variants filtered with over 1000 reads - Githubissues

greenelab / pdx_exomeseq

Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models

MIT License

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Prepare table of variants filtered with over 1000 reads #45

Closed gwaybio closed 6 years ago

gwaybio commented 6 years ago

It looks like the filtered max variants are mostly on the mitochondrial chromosome and ribosomal dna

Func.refGene	intergenic
GL000220.1	10
MT	92

with sample membership:

Sample	Count
032-F5	7
006-F5	6
032-F0	6
048-F0	5
006-F0	5
048-M1-F0	5
008-orhtotopic-met	4
048-M1-F5	4
030-F5	4
005-M-F0	4
008-F0	4
030-F0	4
001-F0	4
005-M	4
008-M2-F0	4
008-M1-F5	4
008-M2-F5	4
048-F5	4
008-M1-F0	3
040-F0	3
008-orthotopic	3
005-M-F5	3
001-F5	3
008-F5	2
029-F5	1
004-M	1
040-F5	1