Question: -m is not work in vcf-compare option
0
gravatar for Anop Singh Ranawat
4.0 years ago by
India
Anop Singh Ranawat0 wrote:

-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:�'���_�#���CO�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�MVg<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 snp rna-seq next-gen • 1.4k views
ADD COMMENTlink modified 4.0 years ago by Pierre Lindenbaum119k • written 4.0 years ago by Anop Singh Ranawat0
0
gravatar for Pierre Lindenbaum
4.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

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...

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Pierre Lindenbaum119k
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