NationalGenomicsInfrastructure/aliceflow

Name: aliceflow

Owner: National Genomics Infrastructure

Description: NextFlow framework to streamline the Genalice variant call pipeline

Created: 2016-07-25 08:05:31.0

Updated: 2016-12-12 15:27:11.0

Pushed: 2017-09-27 07:27:00.0

Homepage: null

Size: 343

Language: Groovy

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README

aliceflow

NextFlow framework to streamline the Genalice variant call pipeline

Having two sets of calls, A and B:

calls only in B:

vcfintersect -r ref.fasta -v -i A.vcf B.vcf

calls only in A:

vcfintersect -r ref.fasta -v -i B.vcf A.vcf

calls both in A and B (intersect):

vcfintersect -r ref.fasta -i A.vcf B.vcf

union calls:

vcfintersect -r ref.fasta -u A.vcf B.vcf

ps -eo pmem,pid,pcpu,rss,vsz,time,args | sort -k 1 -r| less -S

perl -pi -e 's/chr//' PL.vcf

Generated calls that ar in NIST, but not in GATK

vcfintersect -r ~/genome/human_g1k_v37_decoy.fasta -v -i PL.vcf NIST.vcf > NIST_not_GATK.vcf

then calls that are in NIST, and in GA (and not in GATK):

vcfintersect -r ~/genome/human_g1k_v37_decoy.fasta -i NIST_not_GATK.vcf GA.vcf > GA_NIST_not_in_GATK.vcf

calls that are in GA only, neither in GATK or NIST:

vcfintersect -r ~/genome/human_g1k_v37_decoy.fasta -u NIST.vcf PL.vcf > NIST_U_Plat.vcf # get the union (KILLED, can't do that)

calls in GA but not in NIST

vcfintersect -r ~/genome/human_g1k_v37_decoy.fasta -v -i NIST.vcf GA.vcf > GA_compl_NIST.vcf

n of calls:

3642054 NIST.vcf 3953641 PL.vcf 4564558 GA.vcf

172054 NIST_not_GATK.vcf
141543 GA_NIST_not_in_GATK.vcf