Question: SNPs and DEL/MNP in the same position. (DEL or SNP ??)
0
gravatar for sami
12 days ago by
sami20
sami20 wrote:
POS      VARIANTS    REF              Allele Variations
99162    DEL/MNP     TCGGTGTGCGCGG    TCGG
99166    SNP         T                C

I have on my VCF: DELETION in position 99162 and SNP in position 99166.

It is impossible to have deletion in 99162 and snp in 99166 in the same time. How can i explain that ?? Should i keep snp or deletion in my vcf? Please help me

Thank you for your answer.

mpileup snp calls indels vcf • 164 views
ADD COMMENTlink modified 12 days ago by RamRS28k • written 12 days ago by sami20
1

It is impossible to have deletion in 99162 and snp in 99166 in the same time

Not really. One strand can have a deletion while the other has an SNV.

ADD REPLYlink modified 12 days ago • written 12 days ago by RamRS28k

99162 DEL TCGGTGTGCGCGG ----------TCGG*** (1)

99166 SNP --------T------------------------------------- C** (2)

T became C , but in (1) T is absent (deletion of TGTGCGCGG) : It is possible ???!!

ADD REPLYlink modified 12 days ago • written 12 days ago by sami20

I can't understand how One strand can have a deletion while the other has an SNV in the same position !!!! really ?

ADD REPLYlink modified 12 days ago • written 12 days ago by sami20
1

Please don't use bold text, it is bad etiquette. My guess is, this is a repeat region where either this sort of deletion/SNV is a possibility, or the caller gets confused enough that it makes ambiguous calls.

ADD REPLYlink written 12 days ago by RamRS28k

I would check the position in IGV - it is usually much more clear to check them visually.

ADD REPLYlink written 12 days ago by German.M.Demidov1.8k

Can't check 1000 VCF.i need solution to filter this situation => Keep del or keep snp !!

ADD REPLYlink written 12 days ago by sami20

check one BAM file, you don't need to check 1000 of them to understand the situation

ADD REPLYlink written 12 days ago by German.M.Demidov1.8k

I have 1000 strain , so 1000 bam different . The situation is that : we have snp and deletion in the same position . So i have to delete one and keep one. I need the solution!

ADD REPLYlink written 12 days ago by sami20

my recommendation remains the same: check 1 variant in 1 sample in IGV and then you'll understand the situation. After that - extrapolate the conclusions for all 1000 samples.

ADD REPLYlink written 12 days ago by German.M.Demidov1.8k

POS------- VARIANTS -----REF ---------------Allele Variations

99162-------DEL/MNP -TCGGTGTGCGCGG ---TCGG

99166--------- SNP ------------- T--------------------- C

WHAT DO YOU THINK ABOUT THIS SITUATION ?? THERE IS CONFLICT OR NO ?

ADD REPLYlink modified 12 days ago • written 12 days ago by sami20

Check it in IGV :) as @RamRS explained it is totally fine for diploid organisms

ADD REPLYlink written 12 days ago by German.M.Demidov1.8k

I work on bacteria, so not diploid

ADD REPLYlink modified 12 days ago • written 12 days ago by sami20
2

It can be a repetitive region in your bacteria or segmental duplication as well. It may be an assembly problem, not a variant caller problem

ADD REPLYlink written 12 days ago by German.M.Demidov1.8k

assembly! no i do not assembly , just mapping and variant calling . repetitive region mm i don't think because TCGGTGTGCGCGG became TCGG in the variant 1 and 5th T of TCGGTGTGCGCGG became C in the second variant. So we can see that there is no repetitive region in TCGGTGTGCGCGG

ADD REPLYlink modified 12 days ago • written 12 days ago by sami20

can't find 99162-99166 on IGV i must put the name of the chromosome! what is that ! can you explain me ! please

ADD REPLYlink written 11 days ago by sami20

Yes. You need to put chromosome name. e.g. chr4:99162-99166. That interval is too small so IGV will likely show you a larger interval in window. Make sure the chromosome name is the same as in your IGV genome.

ADD REPLYlink modified 11 days ago • written 11 days ago by genomax87k

i think there is only one chromosome in bacteria. (i have reference genome .fasta and file.bam and file.bai) so what should i do ? , thank you!

ADD REPLYlink modified 11 days ago • written 11 days ago by sami20

Genome File Error The following files were not loaded ... reference.fasta ERROR: index file must also be selected

ADD REPLYlink written 11 days ago by sami20

Done , i have now my genome and the region 99162-99166 , but i can't see mapped reads,

ADD REPLYlink written 11 days ago by sami20

Hi, we don't need live updates. Please make as much progress as you can and let us know when you really need help.

ADD REPLYlink written 11 days ago by RamRS28k

I have 0 mapped reads in IGV. I can't see reads

ADD REPLYlink modified 11 days ago • written 11 days ago by sami20

Are you looking at the BAM for the sample that had this set of DEL/SNP variants?

ADD REPLYlink written 11 days ago by RamRS28k

Yes , the BAM is good , but IGV show empty BAM (0,0)

ADD REPLYlink written 11 days ago by sami20

You need to get in touch with a bioinformatics expert close to you so they can look at your computer with you. I don't think we can be of any more assistance to you here.

ADD REPLYlink written 11 days ago by RamRS28k

Is your BAM sorted by co-ordinates and indexed?

ADD REPLYlink written 11 days ago by genomax87k

Yes, I think there is something wrong during variant calling. I whould like to know if i should index my vcf and when ? thank you

ADD REPLYlink written 10 days ago by sami20

BAM and VCF are two different kinds of files. You can visualize both in IGV. If you load your sorted and indexed BAM alignment you can go to that location and inspect all reads there to see the two changes being called in your VCF.

Keep in mind that you are sequencing multiple copies of the genome so different copies may have different mutations in them.

ADD REPLYlink modified 10 days ago • written 10 days ago by genomax87k

should i index vcf ???

I can't add more comment here :/ the limit of the conversation

ADD REPLYlink modified 10 days ago • written 10 days ago by sami20

Between 2 and 3 you need to sort and index the alignment file before calling SNP.

ADD REPLYlink written 10 days ago by genomax87k

Final warning: CAPS and bold are bad etiquette. Keep this up and your account will be suspended.

ADD REPLYlink written 12 days ago by RamRS28k
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