Hello,

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 the HSCHR*. I could fetch sequences for chr1-Y but it does not fetch for MT and HSCHR* and GL000*.1

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 KIFC1".

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.

Thanks