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hyunminkang / cleancall

Correction for DNA contamination in genotype calling
MIT License
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Problems with processing RNAseq data #7

Open maxx19960107 opened 5 years ago

maxx19960107 commented 5 years ago

Hi there, Thank you for creating cleancall. I have some problems when analysis RNA-seq data: The result file is as follows. image

How can I get the contamination results of RNA-seq? I only want results that don't need correction. or is there any problem with my running method? ''' prod 11:48:21 R290-1: /mnt/GenePlus001/prod/maxx/software/contamination4/dbsnp $ cat dbsnp_pileup.sh /mnt/GenePlus001/prod/maxx/software/cleancall/bin/cctools pileup -loci /mnt/GenePlus001/prod/maxx/software/contamination3/dbsnp_138.b37.vcf.gz -index 180022992FR1 -out 180022992FRdbsnp_pileup -ref /products/repos/prod/Akso/BNC_v2/BNC/program/NoahCare/db/alignment/tgp_phase2_flat/hs37d5.fa --run 1 & prod 11:49:17 R290-1: /mnt/GenePlus001/prod/maxx/software/contamination4/dbsnp $ cat dbsnp_verify.sh /mnt/GenePlus001/prod/maxx/software/cleancall/bin/cctools verify -index /mnt/GenePlus001/prod/maxx/software/contamination4/dbsnp/180022992FRdbsnp_pileup.ped -o 180022992FR_verify -vcf /mnt/GenePlus001/prod/maxx/software/contamination3/dbsnp_138.b37.vcf.gz --run 1 '''