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hsinnan75 / MapCaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
MIT License
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BWAmem vs Mapcaller mapping stats #72

Open danessel opened 2 years ago

danessel commented 2 years ago

Hi, having a fast aligner and variant caller is very much appreciated. However I've been looking into the different map stats between BWAmem and Mapcaller and there is quite a difference in mapping rates: samtools flagstat HZK_11-0735_S122_R1.fastq.gz.SolyntusV1.1.mapc.bam 50358636 + 0 in total (QC-passed reads + QC-failed reads) 50358636 + 0 primary 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 0 + 0 primary duplicates 36278106 + 0 mapped (72.04% : N/A) 36278106 + 0 primary mapped (72.04% : N/A) 50358636 + 0 paired in sequencing 25179318 + 0 read1 25179318 + 0 read2 24849642 + 0 properly paired (49.35% : N/A) 24849642 + 0 with itself and mate mapped 11428464 + 0 singletons (22.69% : N/A) 0 + 0 with mate mapped to a different chr 0 + 0 with mate mapped to a different chr (mapQ>=5)

samtools flagstat HZK_11-0735_S122_R1.fastq.gz_SolyntusV1.1.bwa.bam 52365809 + 0 in total (QC-passed reads + QC-failed reads) 50358636 + 0 primary 2007173 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 0 + 0 primary duplicates 51206861 + 0 mapped (97.79% : N/A) 49199688 + 0 primary mapped (97.70% : N/A) 50358636 + 0 paired in sequencing 25179318 + 0 read1 25179318 + 0 read2 40314272 + 0 properly paired (80.05% : N/A) 48719150 + 0 with itself and mate mapped 480538 + 0 singletons (0.95% : N/A) 6854398 + 0 with mate mapped to a different chr 3738627 + 0 with mate mapped to a different chr (mapQ>=5)

I presume this also has an effect on the variants called. What are your ideas about these differences in mapping rates ?

danessel commented 2 years ago

Maybe i should have mentioned that the sample is a tetraploid heterozygous potato, SNP density 1:20.