User: shajib.sust
shajib.sust • 40
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- United States
- Last seen:
- 5 years, 3 months ago
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- 5 years, 4 months ago
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Posts by shajib.sust
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3
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... Hi,
I have genotyped a single person from Platinum Genome dataset of Illumina. I want to identify the ancestry of this person (NAXXXXXX) using his/her genotyped VCF file and population panel data (e.g. EUR or TSI or CEU) from hapmap. What tool should I use to do that? Any literature explaining the ...
written 5.3 years ago by
shajib.sust • 40
• updated
5.3 years ago by
Philipp Bayer ♦ 6.9k
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... Hi,
I observed that PhaseByTransmission (PBT) can not define the phasing of every genotypes (due to ambiguity) for a family trio. Whereas, ReadBackedPhasing (RBP) can show physical phasing of each individual person. So, my question was can we use both the information of PBT and RBP for a set of loc ...
written 5.3 years ago by
shajib.sust • 40
• updated
5.3 years ago by
Ashutosh Pandey ♦ 12k
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... Dear Jeremy Leipzig,
Thank you very much for your reply... I will be very happy to get some more suggestions from you. Is there anyway to phase all of the child genotypes using both the PhaseByTransmission and ReadBackedPhasing for a given family trio genotype information?
With Kind Regards,
-Ru ...
written 5.3 years ago by
shajib.sust • 40
• updated
15 months ago by
Ram ♦ 32k
5
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... Hi, I have genotyped a trio, and then phased them using PhaseByTransmission of GATK Tools. I have then parsed the output vcf file using BCFTools query command. The output file looks like as follows:
#CHR POS FAT MOT CHILD
20 65288 G/T ./. ./. ...
written 5.3 years ago by
shajib.sust • 40
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