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Illumina / Cyrius

A tool to genotype CYP2D6 with WGS data
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Is there a way to use just a part of cram/bam file to get not-None Cyrius result? #5

Closed muzic194 closed 3 years ago

muzic194 commented 3 years ago

Is there a way to use just a part of cram/bam file to get not-None Cyrius result?

I used sample NA19239 from 1000-genomes, aligned to hg38 in .cram format. 

wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239454/NA19239.final.cram
wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239454/NA19239.final.cram.crai

Result of Cyrius: 

NA19239.final    *15/*17    PASS

When I extracted only chr22 using samtools view: samtools view -C NA19239.final.cram chr22 > NA19239_chr22.cram samtools index NA19239_chr22.cram

Result of Cyrius: 

Sample  Genotype    Filter
NA19239_chr22   None    None

Thanks

cariaso commented 3 years ago

Note that https://github.com/Illumina/Cyrius/pull/6 should offer a significant improvement for your use case

xiao-chen-xc commented 3 years ago

Hi @muzic194, Cyrius uses some other regions of the genome for depth normalization. You can extract a bam using https://github.com/Illumina/Cyrius/blob/master/data/CYP2D6_region_38.bed and Cyrius will work on the extracted bam.