User: er.doug.ragnar

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Posts by er.doug.ragnar

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Annovar coding_change error
... Hi I'm trying to use Annovar coding_change program but I keep getting syntax error, any idea why? perl coding_change.pl S01.exonic_variant_function humandb/hg19_refGene.txt humandb/hg19_refGeneMrna.fa humandb/hg19_MT_ensGene.txt humandb/hg19_MT_ensGeneMrna.fa -out S01 Syntax error ...
annovar coding_change written 12 months ago by er.doug.ragnar0 • updated 12 months ago by Kevin Blighe39k
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Smartpca fst details file interpretation
... Hi I used Eigensoft smartpca and created some files, my doubt is in the FSTdetails file. I understand the fist 3 columns are my data groups and SNPname and the last column is the ratio but in the middle I get a N column and a D column which I don't know what they stand for, any ideas? Also, in the ...
fstdetails smartpca written 12 months ago by er.doug.ragnar0
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Comment: C: Annovar VCF annotation syntax error
... I worked out my own error so I will put the correction here for anyone with the same problem: perl table_annovar.pl --vcfdbfile AngH01.vcf humandb/ -buildver hg19 -out myanno -remove -protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a -operation g,r,f,f,f -nastring . -vcfinput PS. Databases also ...
written 12 months ago by er.doug.ragnar0
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Comment: C: Annovar VCF annotation syntax error
... Thank you for your answer, I increased the operation resources but I still get Syntax Error perl table_annovar.pl --vcfdbfile AngH01.vcf humandb/ -buildver hg19 -out myanno -remove -protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a -operation g,r,f,f,f -nastring . -csvout -polish -vcfinput Synta ...
written 12 months ago by er.doug.ragnar0
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Annovar VCF annotation syntax error
... Hi , I'm trying to annotate my vcf file using Annovar but I keep getting syntax error, I tried rearranging the argument but I always get syntax error. Am I doing the command wrong do I have to convert it to Annovar input formt? perl table_annovar.pl --vcfdbfile ./AmH01.vcf humandb/ -buildver h ...
vcf annovar written 12 months ago by er.doug.ragnar0 • updated 12 months ago by Kevin Blighe39k

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