-m is not work in vcf-compare option
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0
Entering edit mode
7.2 years ago

-m is not work in vcf-compare option

vcf-compare -m *.vcf.gz

Missing argument in sprintf at /usr/local/bin/vcf-compare line 142.
Invalid conversion in sprintf: "%\232" at /usr/local/bin/vcf-compare line 142.
Missing argument in sprintf at /usr/local/bin/vcf-compare line 142.
Invalid conversion in sprintf: "%\362" at /usr/local/bin/vcf-compare line 142.
Missing argument in sprintf at /usr/local/bin/vcf-compare line 142.
Invalid conversion in sprintf: "%\026" at /usr/local/bin/vcf-compare line 142.
Expected 1 column names, found [??�?BC?�(�}{o�Ȗ�ߙOA�`0    Fq��,V��n@�?�m��R���??-�6o˒V����|�=��EI��$
                                                                                                  �}qc��T<<�:�z��<���q:�?'���_�#���C?O�EpBm�l�&@����08��gn���5z����G���ç˫����    q)?��c0&������#�4{��p�t2����??��?�E8��ͧ�`�x=��/�d�������Ŭ��/���d�?? M�/G����i���h2�%��藘�pq??��`
<������?_������!���V�u?�\N?�S0o�?�p?���'����.O���Qpd�#k������wvw[����ܚM�?����l:_?#+�h�?:���h�?���S����5�����0�>�?�(?���|W`�������}N�o%�?��??�a��B�����3��?w���5}���I`E�/�q[�?��s`~�?f8��y`��q�?��?^-�?N��Bo��T?��
                                            ?��Xh    ?]�Cl=�H���z�p<�<�2?��%??nK}�?���{�^{��DJ;S�M?Vg<Ɓu;��I۲���r�8�0jY?���5hY?��MA��a�r��s����:��-�a
                                                                                                                                                          �>�#�jw:].
 at /usr/local/bin/vcf-compare line 32.
    main::error('Expected 1 column names, found [\x{1f}\x{8b}\x{8}\x{4}\x{0}\x{0}\x{0}\x{0}\x{0}\x{ff}\x{6}\x{0}BC\x{2}\x{0}\x{f5}(\x{ed}}{o\x{db}\x{c8}\x{96}\x{e7}\x{df}\x{99}O...') called at /usr/local/bin/vcf-compare line 142
    main::read_mappings_list('clinvar.vcf.gz', 'ARRAY(0xac0ee0)') called at /usr/local/bin/vcf-compare line 163
    main::compare_vcfs('HASH(0xac0b50)') called at /usr/local/bin/vcf-compare line 22
sequencing next-gen SNP RNA-Seq • 2.2k views
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Entering edit mode
7.2 years ago

option -m is defined as "... Use with -g (compare genotypes) . The argument to this options is a comma-separated list or one mapping per line in a file. The names are colon separated and must appear in the same order as the files on the command line." http://vcftools.sourceforge.net/perl_module.html#vcf-compare

you just gave a list of vcf on the command line...

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