Feat/support passing index files – githubmemory

v1.10 brought about the new -X option (-X include customized index file), to samtools.

Is it possible to request for tabix/bcftools/etc?

Use case would be for passing in signed s3 urls into all of the various tools.


tabix <signed_vcf_url> -X <signed_vcf_tbi_url> chr2
bcftools view <signed_vcf_url> -X <signed_vcf_tbi_url> chr2
samtools view <signed_bam_url> -X <signed_bam_bai_url> chr2

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