Understand Samtools View Output
samtools view BAMFILE chr2:1,000,000-2,000,000
Hi I use the above command to get an output but I don't understand the meaning.
6197WAAXX100111:2:80:17948:14261 163 chr21 38781704 99 101M = 38782013 409 AAATACATATATTGAATATGTGGATAAAATCACTAGAATATATTCGTGCAATAACATCTACGTGAGACATGACAGCATCTCACCATGTCTGGCAGTCTCTC ;=>==<???@@ABBCDCDDEDEFEEEFFFEDECEEEFFEEEEEED>EEEEFEEFDFCDFED<EEFEFCFEEEDFEFDBDCEFAEDDCC@BBAD@AA>A>?< RG:Z:6197W.2 E2:Z:GGGGGAGGGGGGGTGGGGGTGTTGGGGGCGAGAGCAGTATGCGGATGTACTATCACGAGCAAGTGATATGTCAGAAGCAAACAAGGTAAGTTAGACAGAGA OQ:Z:CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCBCCCCCCCCCDCCCCB@CBCCBCDDBAABB@C>BBAAB>A PG:Z:6197W.2 NM:i:0 UQ:i:0
There are so many columns. Thanks for help.
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1 answer
Sam format: column information:
- QNAME: Query name of the read or the read pair
- FLAG: Bitwise flag (pairing, strand, mate strand, etc.)
- RNAME: Reference sequence name
- POS: 1-Based leftmost position of clipped alignment
- MAPQ: Mapping quality (Phred-scaled)
- CIGAR: Extended CIGAR string (operations: MIDNSHP)
- MRNM: Mate reference name (‘=’ if same as RNAME)
- MPOS: 1-based leftmost mate position
- ISIZE: Inferred insert size
- SEQQuery: Sequence on the same strand as the reference
- QUAL: Query quality (ASCII-33=Phred base quality)
FURTHER DETAILS OF SAM FORMAT: http://samtools.sourceforge.net/SAM1.pdf
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Please read http://samtools.sourceforge.net/SAM1.pdf.
The link is broken for me.
My question is not for sam file's format. My question is that if I use the command samtools view -o output.txt bam region Then in the output file, there are many columns. I don't know the meaning. It is different the sam file's format.
I have the same question, did you figure this out? The output for using samtools view is different than the straight samtools format columns...