Here is the exact command
bcftools norm -f /path/hg19/ucsc.hg19.fasta -c s ./user1.vcf -o ../fixed/user2.vcf
When I run it in the shell directly it works fine.
When i put it into a bash script it fails
The error message comes from bcftools itself
[main] Unrecognized command.
Script is encoded in ascii:
#!/bin/bash
bcftools norm -f /path/hg19/ucsc.hg19.fasta -c s ./user1.vcf -o ../fixed/user2.vcf
So bcftools accept argument when received directly from prompt but not within the script. It is like spaces from prompt and from script are not interpreted the same way
Is that the full error message? Usually after 'Unrecognised command' it gives which command is unrecognised. Looking at the C source:
fprintf(stderr, "[E::%s] unrecognized command '%s'\n", __func__, argv[1]);
So there should be something inside single quotes - the argv[1] in the code.
The most common reason in web chatter for this message is that certain commands are not available in early versions of bcftools. So, do you have more than one version of bcftools installed?
Comment (above) by the OP confirms that an alias referred to an earlier version.