some problems when running sort_vcf_same_as_bam.sh

[Wangdc-Daniel]

Hi
Can I ask how to solve this problem when i was running sort_vcf_same_as_bam.sh
[E::bcf_hdr_read] Input is not detected as bcf or vcf format
sort_vcf_same_as_bam.sh: line 146: 25158 Done(1)

[ghuls]

Probably you gave the wrong order of arguments.

[ipatop]

Hi!

Thanks for writing this scripts they are really useful!

I write because when I run "running sort_vcf_same_as_bam.sh" I get the following error:

/bardata1/anem/scripts/popscle_helper_tools/sort_vcf_same_as_bam.sh: line 176: syntax error near unexpected token (' /bardata1/anem/scripts/popscle_helper_tools/sort_vcf_same_as_bam.sh: line 176: cat <('

Thanks!

[ghuls]

@ipatop Are you running it with bash v4?

[nich-sugiarto]

I am getting a similar issue, and I am using bash v4.2.46

bash --version
GNU bash, version 4.2.46(2)-release (x86_64-redhat-linux-gnu)
Copyright (C) 2011 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>

This is free software; you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

[ghuls]

@nich-sugiarto Can you show the full commandline and error message?