pysam

Pysam is a genomic file toolkit for reading and writing alignment and variant files, essential for NGS data processing pipelines.

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95/100

Security score

The pysam skill was audited on Feb 28, 2026 and we found 5 security issues across 2 threat categories. Review the findings below before installing.

low line 39

Fetch to external URL

SourceSKILL.md

39	for read in samfile.fetch("chr1", 1000, 2000):

low line 57

Fetch to external URL

SourceSKILL.md

57	sequence = fasta.fetch("chr1", 1000, 2000)

low line 163

Fetch to external URL

SourceSKILL.md

163	samfile.fetch("chr1", 999, 2000) # 0-based: positions 999-1999

low line 164

Fetch to external URL

SourceSKILL.md

164	samfile.fetch("chr1:1000-2000") # 1-based string: positions 1000-2000

low line 259

External URL reference

SourceSKILL.md

259	Official documentation: https://pysam.readthedocs.io/

Scanned on Feb 28, 2026

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Categorydata analytics

UpdatedMay 13, 2026