An experiment looking into the effects on mapping statistics and SNV calling with bwa kmer -k sizes 16-23.

Conclusions

SNV Calling

The effect of altering bwa mem2 meme kmer -k sizes has neglible effects on calling all classes of SNVs (SNPts, SNPtv, INS, DEL, Indel), with a small gain seen in -k 16. However, this gain comes at a 30% (47m vs 37m) increase in mapping time vs the default -k 19. -k of 15 improves calling vs the default of -k 19 by adding 1 TP, calling 16 fewer FP and 1 less FN. This improvement is likely not worth the substantially longer runtime of bwa.

Alignment Metrics

Of the 167 mapping alignment statistics calculated by alignstats, few are significantly different with changing -k. However, a few, such as the number of unpaired reads does decrease as -k becomes smaller.

SV Calling Impacts?

SV calling has not been assessed here, but the sizable decrease in unpaired reads at -k 15 may indicate SV calling would improve with lower -k.

Methods

• The daylily framework was run on the 30x Novaseq google brain fastqs for HG002.
• bwa mem2 meme was run with -k values from 16 to 23. -k 19 being the default.
• Deduplication was run with doppelmark and variant calling by deepvariant (see v0.5.3 daylily release for commands).
• Alignment statistics calculated with alignstats.

Results

bwa mem2 meme Runtimes

for -k 16 to 23

• Daylily Pipeline Benchmark Data TSV

Number Unpaired Reads

for -k 16 to 23

• Alignstats DATA CSV

SNV Performance w/Deepvariant

for -k 16 to 23

• Concordance Analysis TSV

SNV Raw Data

|SAMPLE-bwa kmer|Target Region Size|TN|FN|TP|FP|Fscore| | — | — | — | — | — | — | — | |HG002-15| 2525727871| 2521853400| 19944| 3854527| 4148| 0.9968845797| |HG002-16| 2525727871| 2521853397| 19945| 3854529| 4177| 0.996880714| |HG002-17| 2525727871| 2521853399| 19950| 3854522| 4168| 0.996881224| |HG002-18| 2525727871| 2521853400| 19949| 3854522| 4164| 0.9968818686| |HG002-19| 2525727871| 2521853400| 19945| 3854526| 4164| 0.9968823874| |HG002-20| 2525727871| 2521853397| 19946| 3854528| 4189| 0.9968790374| |HG002-21| 2525727871| 2521853396| 19951| 3854524| 4164| 0.9968816123| |HG002-22| 2525727871| 2521853397| 19948| 3854526| 4179| 0.996880067| |HG002-23| 2525727871| 2521853397| 19948| 3854526| 4189| 0.996878778|