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report every base in a bam using bed as input
0
Entering edit mode
13 months ago
bioguy24 • 190
Chicago

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
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14 months ago
France/Nantes/Institut du Thorax - INSE…
chrX    153641860   153641860

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

.

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Thank you very much :).

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