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5
votes
1
answer
228
views
1
answer
Calculate average mapping quality at a position
mapping quality mpileup written 10 weeks ago by hpapoli • 70 • updated 10 weeks ago by Gabriel R. • 2.5k
4
votes
0
answers
2.2k
views
0
answers
BWA-mem MAPQ Calculation
mq bwa-mem mapping quality mapq alignment written 2.3 years ago by rfriedman22 • 40 • updated 3 months ago by h.mon ♦ 20k
0
votes
0
answers
410
views
0
answers
which indel to consider
exome mapping quality indel calls cigar value written 16 months ago by Kritika • 260 • updated 16 months ago by Pierre Lindenbaum ♦ 113k
12
votes
4
answers
3.7k
views
4
answers
How to select aligned reads below certain mapping Quality (from BWA)?
alignment samtools mapping quality bam bwa written 2.1 years ago by kirannbishwa01 • 860
4
votes
0
answers
3.2k
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0
answers
All the reads aligned using STAR have low mapping quality (0-3). What is happening?
alignment mapping quality bwa star written 2.2 years ago by kirannbishwa01 • 860
1
vote
1
answer
1.2k
views
1
answer
What is the difference between the "match score", the mapping quality score under the tmap mapping pipeline
mapping quality match score tmap alignment score written 2.9 years ago by BioinfoNovice • 90 • updated 2.8 years ago by RamRS ♦ 18k
6
votes
1
answer
1.3k
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1
answer
Why does BWA give different Mapping Quality to identical reads?
alignment mapping quality bwa written 3.4 years ago by Asdp • 40 • updated 3.4 years ago by matted ♦ 6.9k
0
votes
0
answers
1.9k
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0
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Samtools : what is threshold for the mapping quality?
next-gen samtools mapping quality snp written 3.8 years ago by Govardhan Anande • 130 • updated 3.8 years ago by Biostar ♦♦ 20
3
votes
1
answer
1.7k
views
1
answer
Remove both pair end reads with low mapping quality using Samtools
mapping quality samtools written 3.9 years ago by DVA • 480 • updated 3.9 years ago by Devon Ryan ♦ 85k
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