vcf-merge gives empty output or run forever

Question

[ste.arnoux]

Hi everyone I have this problem since few weeks now. I try to run a vcftools-merge (because I have vcf fils with sequences data) and it keeps running forever or produce empty output. But no error message. Can anybody help me please?

My vcf files are output from GATK.

​bgzip test1.vcf
bgzip test2.vcf
tabix -p vcf test1.vcf.gz
tabix -p vcf test2.vcf.gz
./vcf-merge test1.vcf.gz test2.vcf.gz | bgzip -c > testout.vcf.gz

The output looks really bad

more testout.vcf ? "?p???v???s??6??-????bA?- ?D?(%????? E?bǽ?]3??W]??n?矟????Xͳu????W~L??狫???C???z?ŷ??lvt????t?????W??7????=????????f???z?G×e޻Z??I??}A6?g?Q0Η??2 ?o>?h??7??e???B?-??`?\,??????o?`?????M\g??m??ͣ???i?=??t??T?? P????h??W?W?Mi????V?????v{}??&??^??z{q???x1Dx??)??u:?˭?7??G?$???,X??^9?.@,??覘?|lDdVvΑ?q??????f????ޓ?7P޺??\?~??q?mQf??^L????{:???_?oiy?.ҧU6R?D?K?U6??QCp??zw???ly???9??????c%^L xQ?Jo?n??t??b?5???????)c0??rT????a???.?uK?//?|bS?w?)()?iW?V$p?l3[??|K??a?^L?.&z???G?

I guess there is some problem but I do everything as mentioned in the tutorial and when I do a vcf-validator my vcf files don't show any error messages.

[Sean Davis]

Silly question, but is the output above from a "more" on the .gz output? That would explain the messiness.

[venu]

May be, you should try zcat testout.vcf.gz | less

[iraun]

Have you tried to extract a small subset of data of each vcf file and perform some tests? For example, select some variants that you know that should be merged (common position) and other variants that are only present in one of the vcf files and check if it works.