Problem Read File .Vcf (For Snp Database)

Question

[hudailkom47]

I have a data like this :

#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    /home/abrari/bioinf/jobs/39/sorting/output.bam
10    389659    .    T    C    4.13    .    DP=2;RPB=9.668049e-01;AF1=0.4999;AC1=1;DP4=0,1,0,1;MQ=42;FQ=4.93;PV4=1,1,1,1    GT:PL:GQ    0/1:32,0,35:31

I was asked to take the data alignment at position 5 before and after the on position 389659, so I asked to take the alignment at before position : 389654, 389655, 389656, 389657, 389658 and at after position : 389660, 389661, 389662, 389663, 389664. how can I get information that align the data? what can be done? whether the data was derived from the file. bam?

Answer 1

[hardingnj]

I think you're asking how to get the aligned reads that may have contributed to this call? Maybe to look in more detail at the MQs etc, put purle guesswork.

Try:

samtools view /home/abrari/bioinf/jobs/39/sorting/output.bam 10:389654-389644

[hudailkom47]

so you mean, I can take from output.bam it? but when I open the file using notepad++, the file seems compressed and unreadable, so i cant get the aligned.