htsget

How to Htsget and IGV.js

You can start local htsget server as follows:

export AWS_PROFILE=dev
sh htsget-rs.sh

curl -s 'http://localhost:3100/reads/service-info' | jq

curl -s 'http://localhost:3100/variants/service-info' | jq

Example Data

You can drop some BAM and VCF into respective folder.

Note that we shall ignore everything except .placeholder file.

Perhaps, grab some from:

• https://github.com/umccr/htsget-rs/tree/main/data
• https://github.com/ga4gh/htsget-refserver/tree/develop/data

wget https://raw.githubusercontent.com/umccr/htsget-rs/main/data/bam/htsnexus_test_NA12878.bam -O ./data/bam/htsnexus_test_NA12878.bam
wget https://raw.githubusercontent.com/ga4gh/htsget-refserver/develop/data/test/sources/giab/HG002_GIAB.filtered.vcf.gz -O ./data/vcf/HG002_GIAB.filtered.vcf.gz

samtools index ./data/bam/htsnexus_test_NA12878.bam
bcftools index --tbi ./data/vcf/HG002_GIAB.filtered.vcf.gz

Dry Run

python3 -m http.server 8888 --directory .

• Go to http://localhost:8888/htsget-igvjs.html

Endpoint

curl -s 'http://localhost:3100/reads/local/bam/htsnexus_test_NA12878' | jq

curl -s 'http://localhost:3100/variants/local/vcf/HG002_GIAB.filtered' | jq

(from remote umccr dev bucket)

curl -s 'http://localhost:3100/reads/umccr-research-dev/validation_data_dragen/SEQC50/SEQC-II_tumor' | jq

Caveats

NOTE 1: how it map bucket and key to htsget ID

export AWS_PROFILE=dev
aws s3 ls s3://umccr-research-dev/validation_data_dragen/SEQC50/SEQC-II_tumor.bam

NOTE 2: UnauthorizedException: Session token not found or invalid

If you find UnauthorizedException: Session token not found or invalid in htsget-rs server log then aws sso login again.

Demo

You are expected to observe as follows.

(Use "Custom" button to load from S3)