pysam

To read and manipulate SAM/BAM alignment files in Python, you can use this Skill to provide a Pythonic interface for genomic data operations. It supports reading, writing, and analyzing SAM/BAM/CRAM formats within bioinformatics workflows.

Querying and filtering VCF variant data is achieved through a Pythonic interface that supports VCF/BCF file formats. You can query, filter, annotate, and subset variant data to streamline genomic analysis and variant calling workflows.

Yes, you can extract reference sequences or specific gene regions from genomic data. The Skill provides sequence file operations to process raw sequencing data and extract targeted genomic regions for downstream analysis.

Yes, you need htslib installed alongside pysam to process CRAM files with Python. The Skill requires both pysam and htslib libraries to perform genomic file operations and manipulate alignment formats.

Calculating read depth at a specific genomic position involves querying alignment files using Python. You can use this Skill to count the read depth at specific coordinates like 'chr1:1234567' by processing SAM/BAM alignment data.