Convert SAM Alignment Records to CSV

Paste SAM text and get a spreadsheet-ready table with QNAME, FLAG, RNAME, POS, CIGAR, decoded FLAG bits, optional tags, and computed coordinate columns.

About this tool

SAM (Sequence Alignment/Map) files are tab-separated alignment records. They are easy for aligners and genome viewers to read, but awkward to paste into a spreadsheet or inspect in a notebook because the columns are positional and the bitwise FLAG field hides useful facts such as paired, unmapped, reverse-strand, secondary or supplementary status.

Paste SAM text here and the tool turns each alignment line into CSV, TSV, semicolon-separated or pipe-separated rows with named columns. Header lines such as @HD, @SQ, @RG, @PG and @CO are skipped. Optional TAG:TYPE:VALUE fields can be expanded into their own columns, joined into one TAGS cell, or dropped.

Worked example

Input:

@HD	VN:1.6	SO:coordinate
r001	99	chr1	7	60	8M2I4M1D3M	=	37	39	TTAGATAAAGGATACTG	*	NM:i:1	AS:i:30

Default output starts with:

QNAME,FLAG,RNAME,POS,MAPQ,CIGAR,RNEXT,PNEXT,TLEN,SEQ,QUAL,FLAG_SUMMARY,NM,AS
r001,99,chr1,7,60,8M2I4M1D3M,=,37,39,TTAGATAAAGGATACTG,*,"PAIRED,PROPER_PAIR,MATE_REVERSE,READ1",1,30

Turn on Add END, REF_SPAN, READ_LEN, STRAND and the same record gets END=22, REF_SPAN=16, READ_LEN=17 and STRAND=+ from POS, CIGAR, SEQ and the reverse-strand flag.

FLAG decoding modes

Summary column: one FLAG_SUMMARY cell listing the set bit names.
12 true/false bit columns: one column per SAM bit (FLAG_PAIRED, FLAG_UNMAPPED, FLAG_REVERSE, and so on).
Summary + bit columns: useful when a table is for both humans and filters.
Raw FLAG only: smallest output.

Limits and edge cases

Maximum input is 20,000 alignment records per run.
This parses text SAM only. It does not read BAM/CRAM binaries, index files, FASTA references or remote URLs.
Each alignment record must contain the 11 mandatory SAM fields. Header-only input is rejected with a clear message.
Optional tags must be in TAG:TYPE:VALUE form, for example NM:i:0 or MD:Z:36.
Space-separated paste is tolerated when at least the first 11 fields survive, but real SAM tabs are safest.
CIGAR validation is limited to syntax and span calculations; the tool does not check the record against a reference genome.

FAQ

What SAM columns are included?

The base table uses the 11 mandatory SAM alignment fields: QNAME, FLAG, RNAME, POS, MAPQ, CIGAR, RNEXT, PNEXT, TLEN, SEQ and QUAL. You can drop SEQ and QUAL for a compact coordinate table, add decoded flag columns, add computed span columns, and keep optional tags as either one TAGS column or one column per tag.

How is the FLAG field decoded?

FLAG is a bitwise sum. The tool checks the standard bits: paired, proper pair, unmapped, mate unmapped, reverse strand, mate reverse, read1, read2, secondary, QC fail, duplicate and supplementary. In summary mode, the set names are joined in one cell; in bit mode, each bit gets a true/false column.

Can this convert BAM or CRAM?

No. BAM and CRAM are binary formats and CRAM may also need a reference genome. This tool is intentionally a lightweight browser-safe SAM text parser. Convert BAM/CRAM to SAM with a bioinformatics tool first, then paste the SAM records here.

What do END and REF_SPAN mean?

When Computed is on, REF_SPAN is the number of reference bases consumed by the CIGAR operations M, D, N, = and X. END is POS + REF_SPAN - 1, the last reference coordinate covered by the alignment. Insertions and soft clips affect the read length but not the reference span.

How do I keep only the tags I care about?

Set Optional SAM tags to Expand one column per tag or Join into TAGS column, then put a comma-separated list in Tag whitelist/order, for example NM,AS,MD. That both filters the tags and fixes their output order, which is helpful when combining multiple runs.

Developer & Automation Access

Run it from the terminal

Same engine as this page, headless — via the gizza CLI:

gizza tool sam-to-csv "@HD	VN:1.6
r001	99	chr1	7	60	8M2I4M1D3M	=	37	39	TTAGATAAAGGATACTG	*	NM:i:1	AS:i:30"

New to the CLI? Get gizza →

Open it by URL

Pre-fill and auto-run this tool with query parameters — the names match the API/CLI:

https://gizza.ai/tools/sam-to-csv/?input=%40HD%09VN%3A1.6%0Ar001%0999%09chr1%097%0960%098M2I4M1D3M%09%3D%0937%0939%09TTAGATAAAGGATACTG%09%2A%09NM%3Ai%3A1%09AS%3Ai%3A30&delimiter=comma&header=true&flags=summary&tags=expand&tag_fields=NM%2CAS%2CMD&include_seq=true&computed=true&mapped_only=true&primary_only=true&min_mapq=0&missing=.

Machine-readable descriptor: tool.json — title + parameters JSON Schema for agents.