View Single Post
Old 03-25-2014, 01:59 AM   #8
jp.
Senior Member
 
Location: NikoNarita.jp

Join Date: Jul 2013
Posts: 142
Question

I tried using MuTect output .bam.out to convert into avinput, however, the format was not proper and I got no annotations after annovar. Moreover, when I used sed '/REJCT/d' input.bam.out > output_file ; it worked and there was no problem. But I want to include 'REJCT' also and filter it out later after annovar is done. Is there something wrong with my commands. The same commands worked after removing 'REJCT' but not working with 'REJECT'.
My commands are:
$ perl ./annovar/convert2annovar.pl -format vcf4 call_status.bam.out > call_status.bam.avinput

$ perl ./annovar/annotate_variation.pl --geneanno call_status.bam.avinput ./annovar/humandb --buildver hg19

$ perl ./annovar/summarize_annovar.pl call_status.bam.avinput ./annovar/humandb/ --buildver hg19 --verdbsnp 137 --ver1000g 1000g2012apr --veresp 6500 --genetype refgene --outfile annovar_snp_annotated.txt --remove
Can somebody tell something ?
thank you in advance.
jp. is offline   Reply With Quote