Question: report every base in a bam using bed as input
0
gravatar for bioguy24
5 months ago by
bioguy24190
Chicago
bioguy24190 wrote:

Trying to output all lines (variant or reference) in the bed file using the below command. Most are SNP's but not all. The command does execute and produce the current output which is ok but why is it only 1 line from the bed? Is there a better approach? Using Samtools and Bcftools 1.9. Thank you :).

samtools mpileup -uBI -l in.bed -f ref.fa in.bam | bcftools call -c - > output.vcf

[warning] samtools mpileup option `u` is functional, but deprecated. Please switch to using bcftools mpileup in future.
[warning] samtools mpileup option `I` is functional, but deprecated. Please switch to using bcftools mpileup in future.
Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid

in.bed

chrX    153641860   153641860   TAZ
chr8    100493900   100493909   VPS13B

desired

chrX    153641860   153641860   TAZ     .     A
chr8    100493900   100493909   VPS13B   --- not sure the best output as there is a variant at position 100493904 ----

current

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  xxxx
chr8    100493901   .   C   .   283.236 .   DP=296;MQSB=0.654094;MQ0F=0;AF1=0;AC1=0;DP4=166,122,0,0;MQ=57;FQ=-281.989   GT:PL   0/0:0
chr8    100493902   .   C   .   283.236 .   DP=297;MQSB=0.59164;MQ0F=0;AF1=0;AC1=0;DP4=158,126,0,0;MQ=57;FQ=-281.989    GT:PL   0/0:0
chr8    100493903   .   T   .   283.236 .   DP=301;MQSB=0.579559;MQ0F=0;AF1=0;AC1=0;DP4=168,128,0,0;MQ=57;FQ=-281.989   GT:PL   0/0:0
chr8    100493904   .   A   G   176.009 .    DP=301;VDB=0.000898749;SGB=-0.693147;RPB=0.954547;MQB=0.957085;MQSB=0.579559;BQB=0.698911;MQ0F=0;AF1=0.5;AC1=1;DP4=85,67,83,61;MQ=57;FQ=178.805;PV4=0.814737,0.382434,0.481619,0.4025  GT:PL   0/1:206,0,219
chr8    100493905   .   T   .   283.236 .   DP=303;MQSB=0.610081;MQ0F=0;AF1=0;AC1=0;DP4=169,126,0,0;MQ=57;FQ=-281.989   GT:PL   0/0:0
chr8    100493906   .   C   .   283.236 .   DP=302;MQSB=0.648613;MQ0F=0;AF1=0;AC1=0;DP4=169,128,0,0;MQ=57;FQ=-281.989   GT:PL   0/0:0
chr8    100493907   .   T   .   283.236 .   DP=302;MQSB=0.619396;MQ0F=0;AF1=0;AC1=0;DP4=171,127,0,0;MQ=57;FQ=-281.989   GT:PL   0/0:0
chr8    100493908   .   C   .   283.236 .   DP=301;MQSB=0.664066;MQ0F=0;AF1=0;AC1=0;DP4=169,116,0,0;MQ=57;FQ=-281.989   GT:PL   0/0:0
chr8    100493909   .   C   .   283.236 .   DP=305;MQSB=0.690757;MQ0F=0;AF1=0;AC1=0;DP4=158,130,0,0;MQ=57;FQ=-281.989   GT:PL   0/0:0
bcftools samtools • 171 views
ADD COMMENTlink modified 5 months ago by Pierre Lindenbaum123k • written 5 months ago by bioguy24190
3
gravatar for Pierre Lindenbaum
5 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum123k wrote:
chrX    153641860   153641860

this is an EMPTY interval. See Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems

.

ADD COMMENTlink modified 5 months ago • written 5 months ago by Pierre Lindenbaum123k

Thank you very much :).

ADD REPLYlink written 5 months ago by bioguy24190
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