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2.1 Primary Analysis - Sequence processing

After sequencing, reads are mapped to the human genome reference (GRCh37). Then, there are some filtering steps in which the number of reads decreases until variant calling. Here, we describe how this reduction occurs in each pipeline.

BIER's pipeline

In this pipeline, there are four stages where the number of reads decreases (mapping, filter by mapping quality, remove duplicates and intervals realignment). This table shows reads remaining after these stages.

  • Unordered List Item

CNAG's pipeline

SampleN_reads_forwardN_reads_reverseN_mapped_read_pairs%_mapped_read_pairsN_read_pairs_single_hit%_reads_pairs_single_hit
SGT03831471997314719972709838086.102653341584.31
SGT07727308034273080342345099185.882290403183.87
SGT16127566691275666912366826585.862317078084.05
SGT18729730857297308572555460985.952489459783.73
SGT23030415770304157702625736886.332563941184.30
SGT23829472514294725142538614786.132477329284.06
SGT24129513223295132232536524685.952453954283.15
SGT27430394832303948322624267786.342569340684.53
espinos/results.primary.analysis.1438851699.txt.gz · Last modified: 2015/08/06 11:01 by cespinos
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