Hi,
I am a PhD student and we have a project that requires me to detect
variants in a family suffering from a autosomal recessive ocular disease.
We are using whole exome sequencing approach. We have 4 raw sequence reads,
3 of them from Illumina and 1 from Ion Torrent.
I intend to use GATK for detecting variants.
My query is pertaining to the BAM files that we got after mapping the raw
reads to human ref genome. Do we now need to remove duplicates from these
BAM files (for which I will use Picard) or will I loose necessary data if I
remove duplicates?
I shall be obliged if you could help me resolve the same.
Thank you.
Regards,
Ankur
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