Anyone have recommendations for making a chart like this for sequence capture?
Picard CollectGcBiasMetrics only works for whole genome analysis.
Picard hsMetrics tends do do funny things with window sizes.
I've had some success with a bedtools & custom scripting but can't reproduce other people's material. I'm close, but I don't know if they are right or if I am right.
Also, anyone got any favorite illumina read simulators that creates reads given a bed file and produces a known gc bias? I'm trying to make control data.
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Jon17 •
2 answers
Alfred calculates the reference GC, target region GC and sample GC content. Here is an example, just select "DNA-Seq, Exome" from the reference data set collection and then jump to "GC Content". Command should be:
alfred qc -b targets.bed -r genome.fa -o out.stats.tsv.gz -j out.stats.json.gz exome.bam
May be the function letterFrequency in package Biostrings is a good choice for GC content calculating.
gs_seq <- BSgenome::getSeq(Hsapiens, gr) letterFrequency(gs_seq, "GC", as.prob=TRUE)
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