Sam2Tsv

Sam2Tsv converts SAM (Sequence Alignment/Map) files into TSV (tab-separated values) to facilitate tabular analysis of sequencing alignments.

Key Features:

• Conversion: Transforms SAM alignments into a TSV format by mapping SAM fields to tab-delimited columns.
• Tab-delimited Output: Produces standard TSV output compatible with spreadsheet software and text-processing tools.
• Integration: Distributed as part of the Jvarkit suite, which comprises Java-based bioinformatics utilities.

Scientific Applications:

• Alignment Data Inspection: Enables inspection and manual curation of sequencing alignments in a tabular format.
• Scripting and Analysis: Facilitates downstream analysis with scripting languages such as Python and R by providing TSV input.
• Pipeline Integration: Allows incorporation of SAM-to-TSV conversion into larger bioinformatics workflows that require tabular data.

Methodology:

Parses SAM records and writes corresponding tab-delimited TSV fields.