intersectBed a gtf file with a vcf file

Question

[Susmita Mandal]

Hey all,

I have been trying to intersect a gtf file with a vcf file using intersectBed without using any options. I have edited my VCF, it has the 8 necessary fields and I have added two columns of my own which are read counts from bed files when intersected with a vcf file ( intersectBed -c ). And the intersectBed with the gtf and vcf is working but something weird is happening. All the gtf files are same. Is that weird or usual? I'm checking the difference between gtf files using plain diff. Am i doing some mistake in creating the VCF file or in the intersectBed step? help me

Susmita

[cpad0112]

9 th column is format column and tags should be defined in vcf header and 10th column on wards sample information as per fields/tags defined in 9th column. I think your VCF is not standard vcf as you defined in OP. Please post your edited vcf to know better. Susmita Mandal

[Susmita Mandal]

##fileformat=VCFv4.2
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    129S1   JF1
1   3000176 .   T   G   40.00   PASS    .   0   0
1   3000223 .   T   A   40.00   PASS    .   0   0
1   3000248 rs32640266  G   T   237.81  PASS    .   0   0
1   3000289 rs32137367  T   G   255.31  PASS    .   0   0

[finswimmer]

Hellohttps://www.biostars.org/u/49214/ ,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[finswimmer]

Hello Susmita Mandal ,

could you please post the commands you use and how your input and output files looks like? I didn't understand what you have tried and what your problem is.

Thanks.

fin swimmer

[Susmita Mandal]

This command seems to give me same results in all the samples:

intersectBed -a /home1/Mouse_Reference_genome/NCBIM37.67/Mus_musculus.NCBIM37.67_plus.gtf -b /home1/temp/8/8_SRR_133_forward_intersect.vcf > /home1/Intersect_by_GTF/plus/SRR_133_plus.gtf

The gtf files are identical!

And this command i used to get the VCF before i did some tinkering:

intersectBed -c -split -sorted -a /home1/Strain_specific_SNPs/SNPs_merged.vcf -b /home1/Sorted_BED_SplitbyStrand/129/SRR_133_129_forward_sort.bed > /home1/Intersect_by_VCF/129/SRR_133_129_forward_intersect.bed

Read counts are different for each sample!