Empty avinput files corresponding to multisamples in ANNOVAR
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12 months ago

Hi, I was using ANNOVAR to convert multi sample vcf file to avinput files (annovar format). I used this command :

sudo perl convert2annovar.pl -format vcf4 -allsample -include multisamples1000gPhase1.vcf > multisamples1000gPhase1.avinput

But I got empty avinput files corresponding to 1092 samples, the original vcf file was around 26GB. Why did this happen??? Can someone explain?

annovar annotation 1000g • 336 views
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You should never need to use sudo to run scripts unless the scripts absolutely need admin access (which 99% of what you do won't need). What happens when you don't use sudo?

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