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Realigned bam

humaasifhumaasif University of SaoPauloMember

i am confused about my results for realignment
i followed GATK steps for realignment and now when i am analysing result of realignment in IGV both bam and realigned bam shows same alignment on the intervals marked by realignedtargetcreator
please suggest what is the problem

Answers

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @humaasif‌

    Hi,

    Sometimes IndelRealigner decides the original alignment was the best alignment. It looks like this is what is happening here.
    Also, sometimes intervals are skipped because they are too difficult to realign (typically where coverage is too high).

    -Sheila

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