combine bam files with a vcf file

Question

[anuradharavi10]

Hello, I have sequenced HG002 (Genome In a Bottle) sample using short read sequencing. The reads have been mapped to GRCh37 and I have created a BAM file suing GATK best practise workflow.

I would like to do some benchmarking of Structural Variants > 20bp. I downloaded the VCF file from https://ftp.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/analysis/NIST_UnionSVs_12122017/

I would like to compare my bam file along with this VCF. However i see that the variant calls do not align correctly with my bam file. I want to know if this is the right way to do this or is there some preprocessing that needs to be done before i do this comparison.

Thanks!

[barslmn]

Do you mean you bought the sample from NIST and sequenced it yourself?

[anuradharavi10]

Yes exactly.

[GenoMax]

Did you see the readme from the folder you link above? It say the following

This folder contains v0.5.0 "straw man" of sequence-resolved large indel and structural variant calls >=20bp for the GIAB Askenazim trio. We recommend using these calls critically, since they are likely to contain false positives, false negatives, and inaccurate breakpoints and sequence predictions.

These do not appear to be SV calls for one sample.

[anuradharavi10]

they are for the trio but the VCFs should be able to identify the variants for the individual genomes as well. Or is there a way to link the VCFs?