question for genotying with bcftools

[lynnatsd]

hi,

I am trying to call the genotypes with the mpileup output using bcftools. I found very weird for one SNP, I actually have heterozygous and the DP4 field also indicate so, but the ALT. column output as ".". See example below -

chr10.fa 128479589 . T . 12.3 . DP=147300;AF1=0.496;CI95=0.5,0.5;DP4=60853,1,79189,2;MQ=59;FQ=-9.5;PV4=1,0,0,0.19 PL 18

has anybody have the same problem and know a reason for this? thanks!

- lynn
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The command I am generating the .vcf is

samtools mpileup -ugf hg19.fasta -C50 -d 10000000 test.bam | bcftools view -cg - > test.vcf

samtools and bcftools come from samtools-0.1.14

[blue mood]

i have the same problems ,can anyone give some suggestions?

[nilshomer]

Look at "DP4=60853,1,79189,2;". That says to me that the reads are mostly on the same genomic strand. This is very unlikely unless built-in your experiment design, and is better explained by mis-mapping. That is why it is not being called with high confidence.

[win804]

Look at "DP4=60853,1,79189,2;". That says to me that the reads are mostly on the same genomic strand. This is very unlikely unless built-in your experiment design, and is better explained by mis-mapping. That is why it is not being called with high confidence.

Then why PV4 for strand bias is 1? I suppose the p-value for strand bias should be very small? I am sorry, probably I misunderstand the p-value for strand bias. but can you enlighten me please? Thanks.

[nilshomer]

Then why PV4 for strand bias is 1? I suppose the p-value for strand bias should be very small? I am sorry, probably I misunderstand the p-value for strand bias. but can you enlighten me please? Thanks.

I think the -S option in mpileup gives strand bias p-values. Is that turned on?

[lh3]

http://sourceforge.net/mailarchive/forum.php?thread_name=4E177430.7030802%40bcgsc.ca&forum_name=samtools-help

[win804]

http://sourceforge.net/mailarchive/f...=samtools-help

Thanks Heng.
That answers my question.