User: Nandini
Nandini • 890
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Bioinformatician
Develop and maintain pipeline(s) for WES, Targeted gene sequencing, mtDNA NGS analysis
Posts by Nandini
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Comment:
C: Calculate coverage from SAM file
... unfortunately not.
these are really old clinical samples that have been sent across. ...
written 12 months ago by
Nandini • 890
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... I have a really old sam format file that does not have any header or information on what build it has been aligned to. It looks something like this
NS500377:28:H16A7BGXX:3:21410:1181:5368 99 chr11 3000035 255 40M = 3000039 44 GTTTTTCACTGTTTCTCCCCATATTCCAGGTCTTACAGT ...
written 12 months ago by
Nandini • 890
• updated
12 months ago by
onestop_data • 250
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... I know this is irrelevant now but being a part of this project, I feel the need to mention that we did correct for covariates such as age, sex and principal components to adjust for possible population stratification. It is also mentioned in the methods section of the paper ...
written 17 months ago by
Nandini • 890
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C: Convert vcf phased data to plink
... Ah, for now, I was able to sort my issue out using the R package SNPrelate. It takes in the vcf file as input, calculates IBS and then if one feels like it, it can also convert it to PLINK format ! ...
written 18 months ago by
Nandini • 890
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C: Convert vcf phased data to plink
... still the same. I don't think PLINK can handle phased Haplotype file in the format 0|1, where 0 indicates ref and 1 is for the alt allele. Can it ? ...
written 18 months ago by
Nandini • 890
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C: Convert vcf phased data to plink
... No, so this is what I did (playing around with a chunk of chr22)
##convert vcf to plink
./plink --vcf input_genotype.vcf --keep-allele-order --allow-extra-chr 0 --make-bed --out MyData
##tried to calculate IBS using King
/king -b MyData.bed --ibs
The result from above is an ...
written 18 months ago by
Nandini • 890
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Comment:
C: Convert vcf phased data to plink
... thanks Kevin, I try to do that but end up wit a file that has 0 for each individual. ...
written 18 months ago by
Nandini • 890
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... I have a phased haplotype format vcf file that looks like this
##fileformat=VCFv4.0
##reference=human_b36_both.fasta
##FORMAT=
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12891 NA12892 NA12878 NA19239 NA19238 NA19240
22 47812545 rs576981 ...
written 18 months ago by
Nandini • 890
• updated
18 months ago by
Gabriel R. • 2.8k
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Answer:
C: hg19 interval list
... maybe not on the gatk bundle site. But probably a [liftover][1] should work ?
[1]: https://genome.ucsc.edu/cgi-bin/hgLiftOver ...
written 20 months ago by
Nandini • 890
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... No, we haven't as yet. ...
written 21 months ago by
Nandini • 890
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