Vcf-Tools : Error "Broken Vcf Header, No Column Names?'" if u have this error.... you can use use tabix then http://bioinfoconcepts.blogspot.in/2015/04/tiindexbuild2-fail-to-create-index-file.html after then type vcf-compare a.vcf.gz b.vcf.gz c.vcf.gz
when Error in Trimmomatic command line /usr/local/bin/trimmomatic: line 1: $'PK\003\004': command not found /usr/local/bin/trimmomatic: line 2: $'\bi\203uH': command not found /usr/local/bin/trimmomatic: line 3: syntax error near unexpected token `$'\a\217\245\234D\312\017\265\026\234\311{\234T\315.\204\024\266ת\353\2179\343\354\003PK\003\004'' /usr/local/bin/trimmomatic: line 3:h�uH��\ �� META-INF/MANIFEST.MFM�=� w � ��GSS�V;7.ƕ�ҧ �h��{�����F��N� ��R< ���>��~A�$��- U�ِ +������ �i �}M���i@�F���; ������z C�K�X]�L�=g#�(�D� ��{�T�.� �ת��� PK ' then simple you can adding "java -jar" like this java -jar trimmomatic SE -threads 4 -phred33 input output AVGQUAL:20 SLIDINGWINDOW:5:20 MINLEN:50`;
[ti_index_build2] fail to create the index file for vcf file error in vcftools If you get this error then type 1 )su and type your root password then type 2) tabix -p vcf filename.vcf.gz
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