Whenever I try to add a reference fasta file for computing the GC content in the GetBamCounts function:
my.countsV6
Solved, It's very likely it was an overflow problem that R encounters with files bigger than 2GBs
I manually computed the GC content of all the exonic regions with bedtools:
$ bedtools nuc -fi hg19.fa -bed SureSelect_Human_All_Exon_V6_r2_bed/S07604514_hs_hg19/S07604514_Covered_edit.bed | awk '{$4=""; print $0}' > AgilentV6_exons_GC_count.txt
and than manually added the GC contents column to the my.countsV6 dataframe
True, I agree with Francesco Antonio Tucci as i've faced a similar issue and had to do a workaround. Try to identify the glitch and proceed with that problematic step manually.
A similar problem (https://github.com/vplagnol/ExomeDepth/issues/14) was solved removing the chr from the fasta file
Francesco Antonio Tucci Thank you for the workaround suggestion. May I ask you how you GC-corrected the samples' counts?
The output of your solution is given in percentage value. How does this percentage content in the reference genome (should) affect the counts? How do I add it?
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