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Heather Peng

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Latest activity by Heather Peng
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    Heather Peng commented,

    Gökalp Çelik Can Kockan Thank you for kindly advising the next step. I think something went wrong at the very start (i.e. CrossMap) so decided to take alternative route to approach CHM13 somatic ca...

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    Heather Peng commented,

    I tried all the ways I could think of, still getting the same error.. so I tried to compare the two:cat -A  Homo_sapiens_assembly38.vcf | sed -n '3436p'#CHROM^IPOS^IID^IREF^IALT^IQUAL^IFILTER^IINFO...

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    Heather Peng commented,

    I ran it but it is still returning tsjdk.tribble.TribbleException: Line 94: there aren't enough columns for line  (we expected 9 tokens, and saw 1 ), for input source: sorted_filtered_knownsites.vc...

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    Heather Peng commented,

    Thank you for your fast response! However when `cat -A sorted_filtered_knownsites.vcf | sed -n '94p'`, it did gave me #CHROM^IPOS^IID^IREF^IALT^IQUAL^IFILTER^IINFO$ so I guess it's tab separated al...

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    Heather Peng commented,

    After a series of revising, I got A USER ERROR has occurred: Error while trying to create index for sorted_filtered_knownsites.vcf. Error was: htsjdk.tribble.TribbleException: Line 94: there aren't...

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    Heather Peng commented,

    Gökalp Çelik Thank you so much I'll look into that right now.

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    Heather Peng commented,

    Hello, I'm currently trying to gatk IndexFeatureFile my vcf file, but it reported A USER ERROR has occurred: Cannot read file filtered_knownsites.vcf because no suitable codecs found.When I cat fil...