Hi,
This issue has been reported earlier #55, but there is no answer so I submit a new issue.
In short, the output is different when using bed file to select a position vs when all positions are used. Example:
18:17 goel@pc-t7-130 dep_mercier:pheno_mut$ bam-readcount -b 30 -q 10 -w 0 -f $refcur -l tmp.bed tmp.bam
Minimum mapping quality is set to 10
CUR2G 9659721 T 528 =:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 A:2:23.00:37.00:11.50:0:2:0.03:0.06:251.50:0:0.00:150.00:0.99 C:1:23.00:37.00:23.00:0:1:0.03:0.06:259.00:0:0.00:150.00:0.99 G:208:23.76:37.00:18.68:140:68:0.07:0.07:265.44:140:0.03:147.78:0.34 T:317:39.59:37.00:8.48:162:155:0.47:0.01:27.19:162:0.51:139.31:0.52 N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00
18:17 goel@pc-t7-130 dep_mercier:pheno_mut$ bam-readcount -b 30 -q 10 -w 0 -f $refcur tmp.bam | grep 9659721
Minimum mapping quality is set to 10
CUR2G 9659721 T 410 =:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 A:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 C:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00 G:119:24.10:37.00:22.36:104:15:0.00:0.07:0.00:0:0.00:0.00:0.00 T:291:39.56:37.00:8.65:150:141:0.00:0.01:0.00:0:0.00:0.00:0.00 N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00
It will be really helpful if this can be resolved.
Hi,
This issue has been reported earlier #55, but there is no answer so I submit a new issue.
In short, the output is different when using bed file to select a position vs when all positions are used. Example:
It will be really helpful if this can be resolved.