chr20_KI270871v1_alt in HG38 Broad Variant and Blacklist regions

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3.7 years ago

ahadli.farid ▴ 50

Hello All,

I used HG38 Borad variant for aligning my Chip-Seq files and noticed existence of contigs like chr20_KI270871v1_alt. What are they? Additionally, when I removed the blacklist regions from the resultant BED files using ENCSR636HFF (GRCH38), almost no filtering happened. Now I am worried that this contigs might represent these regions somehow.

Best Regards, Farid Ahadli

ChIP-Seq • 1.1k views

ADD COMMENT • link 3.7 years ago by ahadli.farid ▴ 50

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Hello,

The GRCh38 ALT contigs are recognizable by their _alt suffix. Alternate contigs, alternate scaffold or alternate loci allow for representation of diverging haplotypes in regions that are too complex for a single representation. See the document on the Human genome reference builds for more discussion on the purpose and usage of ALT contigs.

ADD REPLY • link 3.7 years ago by desouzareis.r ▴ 280

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Exactly what I needed! Love you! Guie a man fish, you feed him for a day, teach him fish you feed him for a lifetime!

ADD REPLY • link 3.7 years ago by ahadli.farid ▴ 50

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