SNPs and DEL/MNP in the same position. (DEL or SNP ??)
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2.5 years ago
sami ▴ 30
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

snp indels vcf calls mpileup • 1.3k views
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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.

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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 ???!!

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

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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.

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

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

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

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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!

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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.

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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 ?

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

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I work on bacteria, so not diploid

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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

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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

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

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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.

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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!

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

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

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

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

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

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

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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.

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Is your BAM sorted by co-ordinates and indexed?

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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

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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.

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should i index vcf ???

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

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

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