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tkrahn / extract23

Extract a simulated 23andMe (V3) style file from a Whole Genome BAM file
GNU General Public License v3.0
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Not works with some data from ncbi #8

Closed RasulSrg closed 5 years ago

RasulSrg commented 5 years ago

https://www.ncbi.nlm.nih.gov/sra/?term=SRP132561 Cant extract any data from bam files which are made of fastq using latest BWA and samtools. Ref. fasta is latest GRchr37.75. But "Bam analysis kit" extracts autosomal with no problem.

tkrahn commented 5 years ago

Please make sure that you map the fastq reads against hg19 and NOT GRCh37. There are tiny differences in the nomenclature.

If for some reason you must use GRCh37, then you also need to convert 23andMe_V3_hg19_ref.tab.gz in the GRCh37 format as I've described it in the "Requirements" section. Then it should work.

RasulSrg commented 5 years ago

Please make sure that you map the fastq reads against hg19 and NOT GRCh37. There are tiny differences in the nomenclature.

If for some reason you must use GRCh37, then you also need to convert 23andMe_V3_hg19_ref.tab.gz in the GRCh37 format as I've described it in the "Requirements" section. Then it should work.

thank you, i am sorry, i am new to bioinformatics. delete my issue message please

tkrahn commented 5 years ago

No problem, the different versions of the reference sequences are not always intuitive.