Length: 249250621 Mapped bases: 79586776 Mean coverage: 3.66 Standard deviation: 11.94 I performed samtools mpileup only in the exon target regions of my exon.bed file, manually confirmed that the pileup was only generated in these regions and added zeros when samtools did not print a line at all in a target region (assuming that there is 0 coverage there). Then I took the 4th column from the pileup file (which gives the coverage at the given position) and computed some statistics. The mean coverage was 12.13. These differences can be observed for many chromosomes, also for chrY, where the reported mean coverage is 0.02 and the true mean coverage is 6.29. This was actually what startled me in the first place, since the sample is male. Do you have any explanation for these observations? Thank you Eva |
Name | Length |
Mapped bases | Mean coverage | Standard deviation |
MAL1 | 643292 | 5719973 | 17.88 | 163.06 |
coverageBed -abam test.bam -b test.bed -d | awk '{c+=$8;len+=1}END{print "mappedBases=" c ,"RegionsSize=" len, "meanCoverage=" c/len}'mappedBases=5724205 RegionsSize=317355 meanCoverage=18.0372
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coverageBed -abam test.bam -b test.bed -d | awk '{c+=$8;len+=1}END{print "mappedBases=" c ,"RegionsSize=" len, "meanCoverage=" c/len}'mappedBases=5724205 RegionsSize=317355 meanCoverage=18.0372
samtools mpileup -l test.bed -Q 0 test.bam | awk 'BEGIN{regionLen=317355}{c+=$4}END{print "mappedBases=" c,"meanCoverage=" c/regionLen}'mappedBases=4845542 meanCoverage=15.2685
samtools mpileup -l test.bed -Q 0 test.bam -A | awk 'BEGIN{regionLen=317355}{c+=$4}END{print "mappedBases=" c,"meanCoverage=" c/regionLen}'mappedBases=5724205 meanCoverage=18.0372