vcf file has no snp

[Sourirewang]

1. What were you trying to do? I want to do the variant calling. and my code was "vg call ../Amana_graph.xg -r ../Amana_graph.snarls -k DLS01.pack -s DLS01 > DLS01.vcf".

2. What did you want to happen? The proper vcf file generated.

3. What actually happened? The vcf file generated but it had only header, no snp. So I use the IGV to view bam file (converted from gamp file) and the snp existed.

4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:

Place stacktrace here.

vcf file: ...... ##contig=<ID=PB.12955.1|900_0|path0:1-2705(+)|transcript/4504,length=2705> ##contig=<ID=PB.10296.2|6833_0|path0:4-1051(+)|transcript/41600,length=1050> ##contig=<ID=PB.12527.2|8058_1|path0:1-524(+)|transcript/49498,length=524> ##contig=<ID=PB.8248.1|5697_0|path0:1-1475(+)|transcript/32829,length=1465> ##INFO=<ID=AT,Number=R,Type=String,Description="Allele Traversal as path in graph"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> ##FORMAT=<ID=MAD,Number=1,Type=Integer,Description="Minimum site allele depth"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled probability estimate of the called genotype"> ##FORMAT=<ID=GP,Number=1,Type=Float,Description="Genotype Probability, the log-scaled posterior probability of the called genotype"> ##FORMAT=<ID=XD,Number=1,Type=Float,Description="eXpected Depth, background coverage as used for the Poisson model"> ##FILTER=<ID=lowad,Description="Variant does not meet minimum allele read support threshold of 1"> ##FILTER=<ID=lowdepth,Description="Variant has read depth less than 4"> ##FILTER=<ID=PASS,Description="All filters passed"> ##SAMPLE=<ID=DLS01> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT DLS01

IGV view:

5. What data and command can the vg dev team use to make the problem happen?

6. What does running vg version say?

Place vg version output here

v1.50.1

[glennhickey]

It might be an issue with the .pack file. You can verify the coverage in that with vg depth -k.

[Sourirewang]

It might be an issue with the .pack file. You can verify the coverage in that with vg depth -k.

Thanks for your reply. I used the code "vg depth ../Amana_graph.xg -k DLS01.pack -b 100000 > DLS01_pack_depth.txt". Here are my results:

Besides, I also checked the gam by running " vg stats ../Amana_graph.xg -a DLS01.gam > DLS01_gam_stats.txt"

[glennhickey]

I don't know. If you can share the .xg and .pack file with me I will take a look in the debugger.

[netwon123]

I guess you maybe use SV-based graph.