ANGSD: Analysis of next generation Sequencing Data
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Mismatch: Difference between revisions
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(Created page with "Angsd can output mismatch from the reference given: ;Distance from be beginning of the read (posi) ;Distance from the end of the read (isop) ;Strand ;Qscore") |
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Angsd can output mismatch from the reference given: | Angsd can output mismatch from the reference given: | ||
;Distance from be beginning of the read (posi) | ;- Distance from be beginning of the read (posi) | ||
;Distance from the end of the read (isop) | ;- Distance from the end of the read (isop) | ||
;Strand | ;- Strand | ||
;Qscore | ;- Qscore | ||
Run like: | |||
<pre> | |||
./angsd -i my.cram -ref hg19.fa -doMisMatch | |||
</pre> | |||
Output looks like: | |||
<pre> | |||
posi isop qs strand Ref A C G T | |||
0 24 13 0 1 0 2 0 0 | |||
0 24 13 0 3 0 0 0 1 | |||
0 24 13 1 0 1 0 0 0 | |||
0 24 13 1 3 0 0 0 1 | |||
0 24 14 0 0 152 1 4 0 | |||
0 24 14 0 1 0 128 0 0 | |||
0 24 14 0 2 11 2 196 1 | |||
0 24 14 0 3 1 0 2 12 | |||
0 24 14 1 0 20 1 2 2 | |||
0 24 14 1 1 1 200 1 16 | |||
0 24 14 1 2 0 5 118 6 | |||
0 24 14 1 3 0 6 3 164 | |||
0 24 15 0 0 186 1 2 0 | |||
0 24 15 0 1 4 91 0 0 | |||
0 24 15 0 2 8 0 90 0 | |||
0 24 15 0 3 0 1 2 7 | |||
0 24 15 1 0 14 1 0 0 | |||
0 24 15 1 1 0 93 1 2 | |||
0 24 15 1 2 0 2 79 2 | |||
</pre> | |||
Revision as of 12:17, 27 March 2015
Angsd can output mismatch from the reference given:
- - Distance from be beginning of the read (posi)
- - Distance from the end of the read (isop)
- - Strand
- - Qscore
Run like:
./angsd -i my.cram -ref hg19.fa -doMisMatch
Output looks like:
posi isop qs strand Ref A C G T 0 24 13 0 1 0 2 0 0 0 24 13 0 3 0 0 0 1 0 24 13 1 0 1 0 0 0 0 24 13 1 3 0 0 0 1 0 24 14 0 0 152 1 4 0 0 24 14 0 1 0 128 0 0 0 24 14 0 2 11 2 196 1 0 24 14 0 3 1 0 2 12 0 24 14 1 0 20 1 2 2 0 24 14 1 1 1 200 1 16 0 24 14 1 2 0 5 118 6 0 24 14 1 3 0 6 3 164 0 24 15 0 0 186 1 2 0 0 24 15 0 1 4 91 0 0 0 24 15 0 2 8 0 90 0 0 24 15 0 3 0 1 2 7 0 24 15 1 0 14 1 0 0 0 24 15 1 1 0 93 1 2 0 24 15 1 2 0 2 79 2