Steve

In the documentation for LoFreq, it is suggested: For Illumina data, we suggest that you preprocess your BAM files by following GATK’s best practice protocol, i.e. that you mark duplicates (not for very high coverage data though), realign indels and recalibrate base qualities with GATK (BQSR). The latter will also add indel qualities, which is needed for indel calling (alternatively use lofreq indelqual). However, GATK has upgraded to version 4, and has dropped many of these tools since they've been...

Thanks Andreas. a significance threshold of 0.01 I was looking in the source code and saw here: https://github.com/CSB5/lofreq/blob/master/src/lofreq/lofreq_filter.c#L1093 if (! no_defaults) { if (cfg.sb_filter.mtc_type==MTC_NONE && ! cfg.sb_filter.thresh) { LOG_VERBOSE("%s\n", "Setting default SB filtering method to FDR"); cfg.sb_filter.mtc_type = MTC_FDR; cfg.sb_filter.alpha = 0.001; } Does this mean that the default Strand Bias filter is at a p-value of 0.001? (cfg.sb_filter.alpha = 0.001) As...

The FAQ page for LoFreq says Do I need to filter LoFreq predictions? You usually don't. Predicted variants are already filtered using default parameters (which include coverage, strand-bias, snv-quality etc). However, I do not see any details about what these default filtering parameters are. Is there a description anywhere? When I try to run lofreq filter --verbose, the only output I get is: Setting default SB filtering method to FDR Setting default minimum coverage to 10 What other criteria are...

I have another question about the SB score values from the .vcf output. It is my understanding that these values are Phred quality scores, which usually are in the range of 0 - 50. However, I am getting many with values of 500 - 1900. Is this expected? And if SB=0 mean no strand bias, then this means that these regions are extremely strand biased? Also, in this thread you state: 2147483647: This corresponds to a p-value close to zero, i.e. a highly significant SNV. What is the meaning of 2147483647...

I have another question about the SB score values from the .vcf output. It is my understanding that these values are Phred quality scores, which usually are in the range of 0 - 50. However, I am getting many with values of 500 - 1900. Is this expected? And if SB=0 mean no strand bias, then this means that these regions are extremely strand biased?

As sources of errors, it takes base-qualities, mapping qualities etc into account. Thanks for this. However I was wondering if there was a more thorough explanation of each of the values that are used in calculation of the 'QUAL' score values that are output in the VCF? I did not see it covered in the publication (maybe I missed it?) and wasn't able to figure out what was going on in the source code.

As sources of errors, it takes base-qualities, mapping qualities etc into account. Thanks for this. However I was wondering if there was a more thorough explanation of each of the values that are used in calculation of the 'QUAL' score values that are output in the VCF?