Toggle first in pair / second in pair

Find SAM flag by property:



  template having multiple segments in sequencing
  each segment properly aligned according to the aligner
  segment unmapped
  next segment in the template unmapped
  SEQ being reverse complemented
  SEQ of the next segment in the template being reverse complemented
  the first segment in the template
  the last segment in the template
  secondary alignment
  not passing filters, such as platform/vendor quality controls
  PCR or optical duplicate
  supplementary alignment

Summary:

Function:
This utility makes it easy to identify what are the properties of a read based on its SAM flag value, or conversely, to find what the SAM Flag value would be for a given combination of properties.

SAM file format:
SAM files contain an optional header section followed by the alignment section. The SAM header is not required, but if it is there, it contains generic information for the SAM file. The alignment section contains the information for each sequence about where/how it aligns to the reference genome. Normally, the alignment section contains 11-12 lines with the following explanations:

1 | QNAME | Query template NAME
2 | FLAG | bitwise FLAG
3 | RNAME | Reference sequence NAME
4 | POS | 1‐based leftmost POSition
5 | MAPQ | MAPping Quality
6 | CIAGR | CIGAR string
7 | RNEXT | Ref. name of the mate/next read
8 | PNEXT | Position of the mate/next read
9 | TLEN | observed Template LENgth
10 | SEQ | segment SEQuence
11 | QUAL | ASCII of Phred-scaled base QUALity+33
*12 | optional fields | variable OPTional fields in the format TAG:TYPE:VALUE

Input:

Input a SAM flag value


Parameters:

① 0x1 template having multiple segments in sequencing

② 0x2 each segment properly aligned according to the aligner

③ 0x4 segment unmapped

④ 0x8 next segment in the template unmapped

⑤ 0x10 SEQ being reverse complemented

⑤ 0x20 SEQ of the next segment in the template being reverse complemented

⑥ 0x40 the first segment in the template

⑦ 0x80 the last segment in the template

⑧ 0x100 secondary alignment

⑨ 0x200 not passing filters, such as platform/vendor quality controls

⑩ 0x400 PCR or optical duplicate

⑪ 0x800 supplementary alignment


Output:

Export explanation results.

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