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  • how to find coverage for PCR-enrichment? (raindance)

    Hi,
    I used Raindance technolofy to entich the exome of chromoxome X. Raindance uses PCR in nanodrops for enrichment.
    Then I sequenced using HiSeq.
    I want to know which of my targets were covered by at least 10 reads, for exmaple, and which targets are not covered.
    I tried to use Picard CollectTargetedPcrMetrics , but got unreasonable results.

    What I did:
    got BAM files from Eland (from the NGS supplier).
    Convereted to picard sorted bam files by SortSam
    and then used CollectTargetedPcrMetrics, with the interval files from raindance:
    AMPLICON_INTERVALS= primers list
    TARGET_INTERVALS= targets list

    Does anyone know what I did wrong?
    I there an alternative free software for this analysis?

    Picard CalculateHsMetrics always worked great for me in whole exome, and I cannot get any help or support from RainDance.

    I will be grateful for any advice!
    Thanks

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