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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Abnormal result from Haplotype caller using reduced representation bisulphite sequencing data



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    Gökalp Çelik

    Hi Jing Qi Chong

    The article specifically states that variant callers using local reassembly such as HaplotypeCaller will have difficulties in adding zero base quality scores into the assembly therefore forcing the engine to add those bases will increase the false positives and may not produce all reliable results. Variant callers that are recommended for the workflow are mostly alignment based callers like samtools or UnifiedGenotyper or haplotype based callers such as freebayes. 

    This statement already tells us that HaplotypeCaller with default parameters may not be suitable for WGBS yet for RRBS. GATK has a beta tool MethylationTypeCaller which may be more suitable for this purpose. 

    Also due to the nature of the regions collected in the RRBS data it may skew the number and types of SNPs present in the output data since WGBS is more complete but RRBS is only a subset of the whole picture. 

    I will relay this question to our team members to get a more in depth response. 



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    Jing Qi Chong

    Thank you so much for your reply, Gökalp Çelik !

    This is helpful, I will try MethylationTypeCaller.

    Not sure if this could be useful but I also ran Platypus (excluding zero base quality score) which used the local reassembly method as well on the RRBS data and the output result has all types of SNPs substitutions. 

    Once again thank you for your response and I hope to hear from you soon.


    Jing Qi

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