Hi All,
Sorry I pressed send too early.
I have very noisy reads and am trying to call SNPs/indels.
I'm runinig into some trouble when truing to use the 'samtools mpileup |
bcftools call' combination.
It seems to incorrectly be calling very long indels where it looks like
there is not support. For example:
'samtools mpileup -f ref.fa sample.bam -r Chromosome:198940-198940'
produces:
Chromosome 198940 C 37 .,.-1A.-1A...-1A.-1A.-1A.,-1a.
-1A.,-1a,-1a.,.-1A,,.-1A,,+1a,+1a,.-1A,,-1a.,-1a,-1a,,-1a,-1a.-1A,-1a.
06?5/<:8>/4<?3691465<3354.08:23:11@3C
This looks fine... however when I try to call the genotype with bcftools I
get a very long indel.
'samtools mpileup -ugf ref.fa sample.bam -r Chromosome:198940-198940 -t AD
| bcftools call -mv' produces:
Chromosome 198940 .
CAAAAGACGTCATCGACGTACGGTCGGTGACCACCGAGATCAACACGTTGTTCCAGACGCTCACCTCGATCGCCGA
C 225 .
INDEL;IDV=32;IMF=0.5;DP=62;VDB=0.145385;SGB=-0.662043;MQSB=1;MQ0F=0;AC=2;AN=2;DP4=0,0,7,2;MQ=60
GT:PL:AD 1/1:255,27,0:0,9
Any idea what is going wrong here?
Thanks in advance,
Jody
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