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BQ of generated reads do not match model specification #11
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@cntrier thank you for this comprehensive report! Will make it easy to replicate and hopefully isolate and fix. |
@cntrier if you use the parameters given in the examples in the Readme, can you replicate the results shown in the Readme? This information is useful to me as a means of understanding if the bug has always been there, or is a recently introduced bug. Thanks! |
@cntrier thank you so much for this report - this is super helpful! I will fix this bug. |
Hi,
I've created a read model with the following script:
mitty create-read-model synth-illumina
100.pkl
--read-length 100
--mean-template-length 250
--std-template-length 20
--bq0 30
--k 200
--sigma 5
And when I check the read model in Mitty with the following:
mitty describe-read-model 100.pkl 100.png
It looks as expected:
But when I generate reads using the model with the following code:
k=HG00632
i=100
mitty -v4 generate-reads GRCh38.p12.fa
./final_vcfs/${k}all.vcf.gz
${k} all_merged_sorted.bed
${i}.pkl
40
7
${k}${i}reads-test.1.fq
${k}${i}-lq.txt
--fastq2 ${k}_${i}reads-test.2.fq
2> vcf-${i}${k}.log
The generated reads have a flat BQ of 9 when I check them with FastQC:
And when I run the god-aligner to create a bam file, I can see in IGV that the reads are a mess. I've tried running different individuals, different read lengths but get the same pattern.
Have I misunderstood something with the read model generation?
Thank you very much for any help you can provide on the matter.
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