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Ana Marija

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Latest activity by Ana Marija
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    Ana Marija commented,

    1. Community
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    3. How to run GenotypeConcordance

    Hello,   I did manage to transfer: new.anamaria.vcf.tar.gz   but when I try to transfer to 2nd file: again.old.vcf.tar.gz   I am getting the error in attach. Can you please let me know why does the...

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    Ana Marija commented,

    1. Community
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    3. How to run GenotypeConcordance

    Hi Genevieve,   I did send my files via ftp server. Can you please check if you received them? One should be named new.vcf.tar.gz and another Nold.vcf.tar.gz   I am not sure if Nold.vcf.tar.gz tran...

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    Ana Marija commented,

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    3. How to run GenotypeConcordance

    sorry for confusion. Let me please explain again: -the old genotype files prior imputation were build 36 and than after the imputation done in 2011 (using Mach) was still on build 36. I lifted thos...

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    Ana Marija commented,

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    3. How to run GenotypeConcordance

    They are both listed to Build 37 using this same file: hg18ToHg19.over.chain.gz downloaded from here: http://hgdownload.cse.ucsc.edu/goldenpath/hg18/liftOver/ old is imputed genotypes done on http:...

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    Ana Marija commented,

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    3. How to run GenotypeConcordance

    are you advising me to do the bellow? gunzip old.vcf.gz gunzip new.vcf.gz gatk IndexFeatureFile --input new.vcf gatk IndexFeatureFile --input old.vcf   and then run: gatk GenotypeConcordance CALL_V...

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    Ana Marija commented,

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    3. How to run GenotypeConcordance

    They are binary files so here it is: head old.vcf.gz.tbi?BCaT=?w\?????Uf?????Q??#"{%{?&{??$??=BrPf6?-??MY?{?w?~?????:???8n?????ݱq?t,Kz?Œ?k?X,????b?e?X?,?K5Ku????????ũ??????lqr?8U?8U?8?Z?jX?jZ?jY??Z...

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    Ana Marija commented,

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    3. How to run GenotypeConcordance

    Thank you for getting back to me, so this is what I did now. I removed all indexed files via: rm *tbi rm *csi Then I indexed it again: gatk IndexFeatureFile --input new.vcf.gz gatk IndexFeatureFile...

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    Ana Marija commented,

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    3. error while running gatk GenotypeConcordance

    the another one was using: java -jar picard.jar GenotypeConcordance CALL_VCF=new.vcf.gz CALL_SAMPLE=0_fam0110_G110 O=gc_concordance.vcf TRUTH_VCF=old.vcf.gz TRUTH_SAMPLE=0_fam0110_G110   but the sa...

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    Ana Marija commented,

    1. Community
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    3. How to run GenotypeConcordance

    Hi Genevieve,   actually I did index .gz files: so this is what I did: bgzip new.vcfbcftools index new.vcf.gz bgzip old.vcfbcftools index old.vcf.gz #SNP concordance module load apps/gatk-4.1.8.1ga...

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    Ana Marija commented,

    1. Community
    2. General Discussion
    3. how to interpret results of gatk Concordance

    Thank you! So does that means that if any SNP that has a mismatch falls into TP?