User: shajib.sust

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shajib.sust40
Reputation:
40
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New User
Location:
United States
Last seen:
5 years, 3 months ago
Joined:
5 years, 4 months ago
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s**********@gmail.com

Posts by shajib.sust

<prev • 4 results • page 1 of 1 • next >
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What tool should I use to identify the ancestry (e.g EUR or TSI or CEU) of a single human using genotyped VCF file?
... 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 ...
hapmap ancestry clustering latest written 5.3 years ago by shajib.sust40 • updated 5.3 years ago by Philipp Bayer6.9k
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is it possible to Improve the Phasing of Family Trios using both GATK PhaseByTransmission and ReadBackedPhasing?
... 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 ...
latest readbackedphasing tool phasing gatk written 5.3 years ago by shajib.sust40 • updated 5.3 years ago by Ashutosh Pandey12k
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Comment: A: How does GATK PhaseByTransmission define the phasing of Father and Mother?
... 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.sust40 • updated 15 months ago by Ram32k
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How does GATK PhaseByTransmission define the phasing of Father and Mother?
... 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     ./.     ./.                             ...
latest phasebytransmission phasing gatk written 5.3 years ago by shajib.sust40

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