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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
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Questions about DP and AF #258

Open zhliUU opened 6 years ago

zhliUU commented 6 years ago

Hi,

After running svtyper, in the VCF file there are DPs in the INFOs. May I ask how the depths are given since when I checked manually the depths very a lot around the breakpoints, especially when the two breakpoints are on different chromosomes. I am trying to get the allele frequencies of gene fusions by SU/DP, do you have any suggestion of getting AFs for gene fusions?

Best,

ryanlayer commented 6 years ago

I am not sure I understand what you are asking. DP is the total depth across a breakpoint. AF is the proportion of chromosomes with the variant in the population that is typically based on genotype. So one is a sample specific and one is population. What were you plans to use DP for AF?

On Jul 25, 2018, at 3:12 AM, zhiwei notifications@github.com wrote:

Hi,

After running svtyper, there are DPs in the INFO. May I ask how the depths are given since when I checked manually the depths very a lot around the breakpoints, especially when the breakpoints are on different chromosomes. I am trying to get the allele frequencies of gene fusions by using SU/DP, do you have any suggestion of getting AFs for gene fusions?

Best,

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zhliUU commented 6 years ago

Hi,

I am trying to get the Variant allele frequency for SV as shown in the figure below. screen shot 2018-07-26 at 9 52 14 am Is that possible to get the VAF for each SV?

Best,

ryanlayer commented 6 years ago

If you have a large cohort, then you can genotype this SV across those samples with SVTYPER. From those genotypes you can get a AF in that population.

On Wed, Jul 25, 2018 at 8:17 PM zhiwei notifications@github.com wrote:

Hi,

I am trying to get the Variant allele frequency for SV as shown in the figure below. [image: screen shot 2018-07-26 at 9 52 14 am] https://user-images.githubusercontent.com/36271531/43237472-8914e964-90bc-11e8-9273-e016c7a2c8c0.png Is that possible to get the VAF for each SV?

Best,

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panzhaodong123 commented 6 years ago

Hi,Ryan, I met the same question.I want to calculate a SV's VAF in one sample,but not in population.how to do,SU/DP?? AND, which reads can be defined as DP?? Thanks

ryanlayer commented 6 years ago

SVTYPER your variant. Then use RO (Reference allele observation count) and AO (Alternate allele observations).

On Mon, Aug 13, 2018 at 1:11 AM panzhaodong123 notifications@github.com wrote:

Hi,Ryan, I met the same question.I want to calculate a SV's VAF in one sample,but not in population.how to do,SU/DP?? AND, which reads can be defined as DP?? Thanks

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panzhaodong123 commented 6 years ago

Thanks, And,I want to know why a SV's RS and AS is zero,while its SR is not zero.

ryanlayer commented 6 years ago

It's hard to say without seeing an example.

On Aug 19, 2018, at 9:16 PM, ZD Pan notifications@github.com wrote:

Thanks, And,I want to know why a SV's RS and AS is zero,while its SR is not zero.

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panzhaodong123 commented 6 years ago

chr1 154142761 22_1 N N[chr6:117642093[ 13724.41 . SVTYPE=BND;STRANDS=+-:1113;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;MATEID=22_2;EVENT=22;SU=1113;PE=579;SR=534 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:1113:579:534:200:13724.41:-1676,-303,-2284:4007:3147:859:3147:859:0:0:0:3147:859:0.21
chr6 117642093 22_2 N ]chr1:154142761]N 13724.41 . SVTYPE=BND;STRANDS=-+:1113;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;MATEID=22_1;EVENT=22;SECON DARY;SU=1113;PE=579;SR=534 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:1113:579:534:200:13724.41:-1676,-303,-2284:4007:3147:859:3147:859:0:0:0:3147:859:0.21

The SV describle as blow.

ryanlayer commented 6 years ago

I'm not sure why this is happening. You may want to try the svtool mailing list.

On Aug 19, 2018, at 9:51 PM, ZD Pan notifications@github.com wrote:

chr1 154142761 22_1 N N[chr6:117642093[ 13724.41 . SVTYPE=BND;STRANDS=+-:1113;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;MATEID=22_2;EVENT=22;SU=1113;PE=579;SR=534 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:1113:579:534:200:13724.41:-1676,-303,-2284:4007:3147:859:3147:859:0:0:0:3147:859:0.21 chr6 117642093 22_2 N ]chr1:154142761]N 13724.41 . SVTYPE=BND;STRANDS=-+:1113;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;MATEID=22_1;EVENT=22;SECON DARY;SU=1113;PE=579;SR=534 GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:1113:579:534:200:13724.41:-1676,-303,-2284:4007:3147:859:3147:859:0:0:0:3147:859:0.21

The SV describle as blow.

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wyy1234-github commented 3 years ago

Hi, I want to calculate a fuison's VAF, but i find AO is not eqal to SU, what's the difference between AO and SU? and which should I use to calculate VAF, SU/DP or AO/DP? thanks!

this is an example: GT:SU:PE:SR:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/0:228:38:190:200:0.00:-139,-9199,-31842:32756:32492:263:32491:262:25334:188:0:7157:74:0.008