I am trying to fetch sequences using an interval file with columns 'chr',
start, end and name.
The names in the chr column are like chr1,chr2...chrY... and for the chrMT and
I could fetch sequences for chr1-Y but it does not fetch for MT and HSCHR* and
I get the error "4536 warnings, 1st is: Unable to fetch the sequence from
'33529672' to '329' for chrom 'HSCHR6_MHC_MCF'."
Skipped 4536 invalid lines, 1st is #775, "HSCHR6_MHC_MCF 33529672 33530001
I locally cached the database as Human Hg19.
Now does ur Hg19 contain MT and the other GL000*.1 and haplotype sequences in
it ? Or do I change the headers of those lines in the interval file accordingly
Id be glad if you could get back to me asap.
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