Extracting codis loci

[Anastassiya Zidkova]

Hi,

I just started to use lobSTR for STR  extractuion from VCF and I am amazed by your work guys!

I just wanted to post modification to your best practice for codis loci extraction, since I found that your pipe is not giving expected results.

Here is my modified pipe:

intersectBed -a $VCF_FILE -b '~/Software/lobSTR-bin-Linux-x86_64-4.0.6/hg19_v3.0.2/lobSTR_codis_hg19.bed' -wa -wb \

| cut -f 1,2,10,14- \

| sed 's/:/\t/g' \

| cut -f 1,2,3,9,15- \

| sed 's/\//\t/g' \

| awk '{print $0 "\t" ($5+($7*$8))/$7 "\t" ($6+($7*$8))/$7}' 

Columns that I selected for final table are: Chromosome, Position, Genotype, Genotype given in bp difference from reference, Repeat period, Reference allele, Repeat name.

I slightly corrected sed by adding `g` at the end, this command should parse Genotype and Genotype given in bp difference from reference columns

I then computed number of repeats using following formula  (Genotype given in bp difference from reference + (Repeat period + Reference allele))/Repeat period.

Here are results that I get:

chr11 2192318 1 1 11 11 4 7 TH01 9.75 9.75

chr13 82722160 1 0 -8 0 4 11 D13S317 9 11

chr15 97374245 1 2 5 45 5 5 PentaE 6 14

Cheers,

Anastassiya

[nageen....@iiu.edu.pk]

Thanks for posting this command. The resulting table has 11 columns. can you please tell the name of each column accordingly??

[Anastassiya Zidkova]

Hello,
column names are following: Chromosome, Position, Genotype x2 (for each
chromosome), Genotype given in bp difference from reference x 2 (for each
chromosome), Repeat period, Reference allele, Repeat name, Number of
repeats x2 (for each chromosome).

Hope it helps,
Anastassiya

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[tfr...@gmail.com]

Hello Anastassiya! I need to extract the genotypes from the autosomal STRs from de 1000 genomes project. Can you help me? I am new in this. Please!!

El lunes, 20 de agosto de 2018, 9:26:15 (UTC-3), Anastassiya Zidkova escribió:

Hello,
column names are following: Chromosome, Position, Genotype x2 (for each
chromosome), Genotype given in bp difference from reference x 2 (for each
chromosome), Repeat period, Reference allele, Repeat name, Number of
repeats x2 (for each chromosome).

Hope it helps,
Anastassiya

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