bcftools index does not support indexing from stdin / stream

[aurmra1]

Hi,

I have been trying to index a VCF using bcftools index from stdin (streaming), but it does not seem to be supported, even when the input is BGZF-compressed.

Here are the commands I tested:

cat PP0087.uber_vep_tabix_qc.2018-12-20.vcf.gz | bcftools index - -o /tmp/index.o
# index: the input is probably truncated, use -f to index anyway: -

zcat PP0087.uber_vep_tabix_qc.2018-12-20.vcf.gz | bcftools index - -o /tmp/index.o
# index: the file is not BGZF compressed, cannot index: -

zcat PP0087.uber_vep_tabix_qc.2018-12-20.vcf.gz | bgzip | bcftools index - -o /tmp/index.o
# index: the input is probably truncated, use -f to index anyway: -

However, indexing the same file directly works as expected:

bcftools index PP0087.uber_vep_tabix_qc.2018-12-20.vcf.gz

Please let me know if I am missing something, or if there is any recommended workaround other than writing the file to disk first.